Joshua + Samuel
This was badly explained.
Look at this dialogue:
(00:05:59)
George Aiken: Samuel, remember our deal. You ever want to see your brother again, you do as I say when I say it. We get Miles, we get the weapons, you and Joshua get your freedom. Clear?
Samuel: Claro.
(00:07:01)
Ray Santiago: The director has no idea you're about to cut a deal.
George Aiken: There is no deal. We use Samuel and Joshua to get to Miles. We bring 'em all down. Nobody's going anywhere, Ray.
So based on that, George offers Samuel and Joshua their freedom in exchange for setting up Miles, but when talking to Ray, George reveals he was never going to honour the deal, but instead "bring them all down".
If this is the case, then why did they transfer Joshua from the prison into a safehouse (see below)? This makes no sense.
(00:11:41)
FBI agent: Someone broke into the safe house. They took Joshua and killed our agents.
Ray Santiago: He did it again.
This leads me to the next problem: According to Ray, Miles (or his accomplice) took Joshua from the safehouse. But why bother with Joshua? Miles doesn't need him, especially not if he was going to kill Samuel instead of reuniting them, and Samuel could never have verified whether Joshua is still with the FBI or with Miles accomplice (proove being the prank phone call when Samuel ends up talking to Miles instead of Joshua).
Anyway you look at it, this does not add up.