The movie certainly could have used some tighter editing and maybe even a couple watch-through to ensure all of the details are closed up. What DID happen to Dr. Connor's boss? We never see him again after the bridge scene!
There seems to have been quite a few cuts in the movie, and that's the most notorious one. There are stills showing that character finding the Lizard's Lair, and Peter fighting Connors there, with the other guy restrained. This is the scene supposedly where all the dialogue about "the truth about your parents", "do you think what happened to you was an accident" etc. from trailers would have gone.