I'm noticing this as well. I have a smart album that looks for photos that were taken with an iPhone and sync that back to my phone so I can clean out the camera roll. The movies from the camera app have no useful metadata so the best I could do is create a smart album that looks for files with a filename that starts with IMG_ and ends with .MOV. That finds them but you can't sync this back to the iPhone. This is a rather large over site on Apple's part and hopefully it will be fixed.
After some digging, page 106 in the user guide:
If you delete the photos and videos from iPhone when you upload them to your
computer, theyre removed from the Camera Roll album. You can use the iTunes
Photos setup pane to sync photos back to the Photos application on iPhone. Videos
cant be synced back to iPhone, however.
Yea... that needs to be fixed.