Continuity mistake: When the X-men ship is trying to dodge the rockets, there are a few close-ups of Bobby showing that the seat in front of him is empty. In other shots before and after the close-ups of Bobby, it shows that Rogue is sitting in that seat.
Continuity mistake: When Nightcrawler tries to stab the president he is in the middle of the table but in the next shot he is at the edge.
Continuity mistake: When Nightcrawler rescues Rogue from falling in mid-air, he dives back into the jet. In the next shot, you can see that the hole in the jet is folding and repairing itself, but a couple of shots later, the hole repairs itself again.
Answer: Presumably he is sensing the presence of Jean/Phoenix.
BaconIsMyBFF