Um, because they had ZERO trust in him not to set them up, botch the deal, etc.
However, they needed him to complete the transaction.
So they used Jed, literally the only person they knew he cared about, as a threat.
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If Roper was suspicious that Jonathan/Andrew would betray him then it would be perfectly rational to assume that Jonathan/Andrew might pull something unexpected, whatever that may be, during the meeting with the clients.
Roper being who he is would believe it's always best to be the one in control, so it would make sense to confront him BEFORE the deal to let Jonathan/Andrew know he knows what he's up do, and has Jed as hostage to make sure the deal goes through without a hitch. Even though it doesn't make any difference in the end as Jonathan/Andrew went and blows up the merchandise anyway.

That's not really a "major" plot hole. It's just part of the plot to get to the end. Roper was becoming very close to Jonathan and treated him like family. Roper usually is never wrong about people so it's natural that he is outraged when he finds out he has been fooled by this person the entire time and at the same time been sleeping with his lover. The confrontation was an outburst and clearly wasn't planned. That is not a plot hole at all.

They wanted to make sure he wasn't wired, and they wanted to make sure he played ball. Roper knew about his affection for Jed, so he knew that as long as he held that trump card, Pine/Birch had to play along. He took his cellphone to prevent any shenanigans not know that Pine had already transferred the money to another untraceable Swiss account.
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You mean "regardless."

Correct. Pine would have done the same thing no matter what they did to him. It was do or die that day.

It doesn't even matter. Jonathan already had his plan in motion and would have proceeded irregardless.

Good point, but they could have arranged a check without being specific to him.
He was not, by the way.
I was born in the house my father built

If Andrew/Jonathan is needed to complete the transaction, why in the world would you confront and expose him BEFORE the transaction?
They wanted to make sure he wasn't wearing a wire.
Tell your god to ready for blood.

Agreed. That was a rather dumb play because you don't know what Andrew/Jonathan might do or say.