There actually isn't anything wrong--he's doing a little bit of exploring on the ship after you've completed the Grissom Academy mission.
Look around the ship and you will have a nice surprise.
SPOILER:
Look in the cargo hold where Jack used to be in ME2. Javik is there doing his thing as a Prothean, following biological markers and when approached will talk to you about the former occupant of that living space.
Enjoy!
