Is there a iOS5 bug regarding the video app forgetting at which time a video has to be resume? After upgrading my iPhone 4 to iOS 5 I recognized, whenever I close a movie mid-play by clicking Done and selecting it again, it will just restart and not remember where it was before.

This was remembered in the previous iOS release when videos where still located in the Music app.

The videos were not purchased through iTunes but converted from avi with ffmpeg (just to be complete).

Is this a known issue?
No - this general behavior wasn't changed in iOS 5 as part of the video / music app split.