When Beckett and McCord find Esposito, Ryan, and Castle in the warehouse, Beckett doesn't recognize the trio until they turn around. Surely she would be able to recognize her fiancé, if not her longtime partners, from behind.
Most of the six people in the warehouse put their prints on the cases or the contents thereof, compromising evidence.
When Castle, Ryan, and Esposito are in the break room watching Beckett and McCord, Ryan comments about Beckett "Her and her partner just hijacked our case". The more grammatically correct structure is "she and her partner", because if the phrase "and her partner" is taken out of the sentence, the resulting "Her just hijacked our case" doesn't make sense.
When CIA agent Ethan Wright confronts the team in the warehouse, he does so with a weapon pointed at them. This could easily have led to him getting shot before he could say anything. Then, when he tosses his credentials to Esposito so they can be verified, he still keeps his weapon pointed at the team. This is long past the point where he should have lowered his weapon, so it would seem very suspicious.