In her flashback at the subway, when they were being arrested the leader of the bad guys looks back and sees the girl with her doll
He smirks which implied that he realized it was in the doll other there was no hard proof.
How he knows the doll was in the coffin I don't know. It seems to be something he figured beforehand. They have been after it for a while even if they were in prison they might have connections on the outside.
Brittany Murphy character did know they were after her, which is why she kept herself institutionalized. And she did seem to know they wanted to know, which is why she'd say thing like you want what they want or I'll never tell.

Yeah, that's probably the best bet.
So many stories, so little time.

That's what I was thinking too because Michael Douglas was looking through the old newspaper articles, so I assumed the kidnappers had also seen or heard the stories of Elizabeth on Hart Island where her father was buried.

Also, they might have seen the newspaper articles about Elisabeth wondering around on Hart Island.

It wasn't a ruby, it was a red diamond far, far, far more valuable than a ruby. But that's beside the point you're right, this is a really big plot hole (among several).

Plus it had been 10 years of them looking for this so you just have to believe that after 10 years they found out that it was in the doll and buried in Elizabeth's Dad's grave, but they just didnt know the number.

Because like the others said its a movie,gotta use your imagination.They patted him down before they pushed him in front of the train and if you remember he was saying I'll tell you where its at if you let me up,or something to that affect,so they figured if it were on him being pushed in front of a train he'd give it up.Then I'm sure they heard the stories of the little girl wondering around on Heart island..so they were figuring maybe he gave it to the little girl???they were checking out every angel,I know I would if I had a ruby worth that much money!

Umm, because it's a suspense movie and suspense movies have plots and plots should make sense. Even though it was a very entertaining movie, the whole premise of Dont say a word or the tagline Ill never tell was based on this secret that the girl has. I can see no logical explanation of how the burglars could have known that she had memorized the number or could have know about the doll in the casket. To find out in the end that it was a secret that the burglars could not have known about was a little disappointing.

its a movie. who needs explanation

They must have guessed cos all they needed was the grave number

Answer attempted in 'stupid questions' - crazydawg - below
there is some reference to them knowing the father didn't have the diamond - but how would they know that? the jerks pushed him in front of a train and seemingly didn't know what was on him