I've been thinking the timing of everything seemed off. Tom walking into custody just as his putative girl friend was planting a bomb implies not just the possibility that he and she somehow planned it together/scheduled it. (No, there's no reason why she would agree to go to jail just to provide Tom an alibi for the Fokin murder, especially since disposing of the murder weapon would have been SOP for any halfway competent assassin.)
The other possibility is that it is because Reddington knew Tom was trying to confront Elizabeth about the box, that Reddington manipulated the whole crisis by hiring Zanetakos in the first place. That would explain how Reddington could plant the photo. Then the whole episode would be Reddington burning off an old business associate to boost Elizabeth's morale. Framing Tom is pretty bad, particularly since it makes her a gigantic fool for being screwed by a criminal. But after all she got over Reddington sending a man to stab Tom.
Reddington's got an inside man at Black Site, maybe part of the fallout from Kuwait.