A couple of characters mention the plane either crashing into or being pulled from the East River. The plane was shown as having crashed on dry land.
When "Berlin" is introduced at the hospital, he talks with an American accent. In season 2, he's transformed into a stereotypical bad guy Russian with the well known Russian movie accent.
When the story of Berlin is being told, he talks about the pocket watch having a picture in it. In the first shot of Berlin opening it, there is no picture inside.
The FBI is trying to identify which of ten prisoners from the crashed plane is Berlin. Three are in custody and four are dead, including one burned beyond recognition. They conclude that Berlin is among the remaining three. However, because one dead prisoner cannot be identified, he cannot be excluded from being Berlin.
If, of the ten prisoners on the plane, three are in custody, four are confirmed dead, one of whom was burned beyond recognition, that leaves four profiles unaccounted for, not three.