Clearly you are very desperate to maintain the probability of any and all of these circumstances. I will leave you to your desperate mission of advocating that this wasn't wholly weak writing.

"what indicated it was highly flammable?" - because the character noticed that some of the gas venting from ship exploded into flames when it touched some of the flames from the bunker explosion! She then decided to make a flaming bottle.
"there would need to be a flame at the mouth to ignite flammable gas" - the burning cloth was sticking out of bottle!
"The ship was not moving at all when it exploded. It was hovering." - so the internal explosions non-linearly destroyed one or more of the internal "hover" engines so causing one side of ship to dip and giving lateral movement while crashing.
"sat there like a dummy" - you seem to be the only one missing all the clues Sherlock.

If you aren't <20 then that's your problem.
Again, what indicated it was highly flammable? Before she threw a molotov in I wasn't really paying close attention by this point because the film had gone full Cloverfield retard already. Did it flame up a car or something?
Ok, first an argument that she only threw the bottle because it carried a bit of flaming paper is truly moronic. Congratulations.
Second, some basic chemistry: there would need to be a flame at the mouth to ignite flammable gas if this creature was filled with flammable gas there wasn't
So either the creature carried at least two liquids that when combined became explosively flammable, but on their own were inert until mixed, or the chemical being carried was volatile when exposed to some gas in our atmosphere, which would be considerably less likely.
In either case the odds of a 'molotov' made out of low burn alcohol and a bit of paper thrown in the mouth would explode the entire ship is moronic. Even more moronic would be just throwing a bit of burning paper in, which you think was enough to do it.
Let's ignore the fact that this is all a very very lazy lift from independence day, and thematically just about every other invasion movie where the weakness reveals itself to be shoot them in the mouth, use seawater etc etc.
The ship was not moving at all when it exploded. It was hovering. To argue that it gained momentum to avoid crashing the hero is as moronoic (that word keeps reappearing) as the Hindenburg going up in flames and zooming off somewhere else before hitting the ground.
None of this weak ass ending made sense or was probable, unless you wanted it to, because realising it was weak would mean you sat there like a dummy and ate it up.

Yes it did contain highly flammable gas as others have explained previously. Just because you didn't notice the signs given in the film as the character did and lots of viewers did doesn't make it stupid, just makes you stupid.
Also you seem to seperate the fact that the bottle of alcohol she threw in was not a molotov cocktail and was in fact irrelevent to the explosion.
The bottle could have been filled with water and it would have had the same effect. The only purpose for the bottle was to give the flaming paper stuffed into it enough momentum, weight and accuracy to throw into the mouth - try throwing a piece of burning cloth/paper on its own and see how accurately and far you can throw it.
Naked flame + flammable gas = explosion
The tentacles dropped the truck at a non-terminal slower velocity.
The ship moved away before it crashed - why would you say it should really fall on top of her???
I'm not 20. Quit with the moronic ad-hominum arguments.

Sorry, I missed the bit where the alien was clearly highly volatile/flammable until it conveniently exploded by ingesting a barely flamamble liquid with a bit of burning paper stuck in it
Note: in this instance, where any of this likely, the alien would have sneezed all that flaming snot down straight on top of her ending this stupid story quite abruptly. Which wouldn't have mattered because being dropped without a seat belt on in your truck from 50-60ft in the air will have a good probability of breaking several bones, or outright killing you. At which point if your survive you still die as the alien spaceship falls on top of you.
As far as weak, stupid film premises go, it's right up there. But it is
Cloverfield
which was clearly made for idiot teenagers that don't know anything, like the flammability of single malt, or the likelihood of destroying an alien spaceship with it. Remember the 23 year old heading off to Japan to take up a role of a CEO for a Japanese company in the first film? If that didn't ring as weak chances are this molotov cocktail made sense to you too, because you're probably about 20. All this alien crap at the end was just Clovefield crap tacked on to an existing and sensible hostage story. Which is why this alien crap felt like unnecessary garbage and high school production level script.

Yes, it is obvious the alien was highly volatile/flamable and she threw a naked flame inside it, so an explosion of volatile chemicals was highly likely.

Definitely the weakest idea in the whole movie. Otherwise not a bad film though.

Who cares if a Molotov cocktail would explode or not? I think the bigger question is why wasn't the war over with humans winning by the time Michelle escaped if their "superior" biological technology is so susceptible to some common earth chemicals mixed in the right proportions? Apparently the aliens just came along, saw our planet and said, "Let's start our invasion now without any planning."
Peace is not the absence of affliction, but the presence of God. ~Author Unknown

This message has been deleted.

It's because the scene required her to throw a molotov cocktail at an alien ship to bring conclusion to her character arc. LOL She starts the film running away from a relationshiprunning away from problems so the only way to reconcile this is to go to Houston to help survivors fight mothereffin aliens? LOL!!!
Yeah makes complete sense.

That was probably the LEAST of my problems with this thing!
I. Drink. Your. Milkshake! [slurp!] I DRINK IT UP! - Daniel Plainview - There Will Be Blood

Of course it makes a difference!!
It clearly showed her picking the bottle off the side when she was leaving her apartment - it was called Glen-something, and had a traditional label which means it was most likely a single malt Scotch Whisky (not Whiskey, which is Irish or American).
Being a single malt Scotch it would be 40-50% alcohol by volume, which burns readily. Wine is 12-15% so will not burn no matter how long you hold a flame to it.
Wouldn't explode but as an ignition source combined with the highly explosive green gas, it made sense.
darker than biscuit, lighter than oak

Thinking outside the box doesn't make molotovs idiot.

you're an idiot. you've never seen those alcohol drinks where the bartender lights the top on fire? Like a flaming B52? Alcohol in higher proofs will catch fire. All she needed to do is light that paper half dipped in the proof and wala she has a constant fire source. Throw that sucker in the belly of the beast who was spewing out highly combustible green gas and then you have a recipe for an explosion. Maybe you should pay better attention next time or i don't know try thinking outside the box for once.

The brand is fictional so we can't say for sure what proof it was, but there are real whiskeys which are over 100 proof and are flammable.

Does it make a beep difference? Whiskey isn't any more flammable than wine and it looks like a beep bottle of wine.

"
Also a bottle of what seems to be wine just happens to be in the car for no reason what so ever. "
Seriously?
It's scotch, not wine. And it is in the truck because Howard took it from Michelle's car after he ran her off the road. She took it off the desk in her house before she ran away from home. Howard even explicitly mentions it.
"Didn't have time to grab the booze, unfortunately"

I made one by farting into a bottle and corking it. But I ate Taco Bell the day before, so

Well first of all she's a fashion designer and in literally 10 seconds she thinks about making a molotov and actually manages to make a working one without
any
prior training or experience (or the actual materials required, but lets leave that aside for now).
Also a bottle of what seems to be wine just happens to be in the car for no reason what so ever.
Wine doesn't catch fire from a beep lighter.
Stuffing paper in a bottle full of wine won't make the paper super-flammable it will make the paper super "unflammable".
Paper barely ever catches fire like that.
You can't make a molotov using paper. Nor wine. Nor any kinda alcoholic beverage.
As for some people who said molotovs explode, well, they aren't supposed to. They are supposed to be tossed to stuff, the bottle is supposed to break and the gasoline inside is supposed to splash around and make that thing catch fire. Of course, the fire might spread from the cloth to the inside of the bottle and if that happens before the bottle is thrown and thus broken it will -quite possibly- explode due to the gasses produced when the gasoline catches fire. But as I said that's not how it's supposed to work.

"Regardless of what she threw there would certainly be no explosion like that I think it's safe to assume the thing was not full of oxygen and therefore could not explode chemically at all! "
How could something filled with oxygen explode? So why would it be safe to say that?
Also: It was very clearly demonstrated that the creature was spraying explosive highly flammable gas . This is why she decided to throw fire into it.