I encountered on several occasions already that what was displayed in pending changes did not match the actual state of files being committed. The reason being that changes are not automatically updated in the UI, but upon commit new changes are automatically collected using default behavior of changed files being committed, added, moved and deleted files must be selected manually - meaning the latter will not be part of such commit. The minimum thing that could be done is to notify the user that there are undisplayed changes that need to be reviewed. Even better would be to add git like staging of changes. I concede that this issues don't occur often and are a case of user being sloppy, but I would also point out that the workflow imposed by the UI doesn't help the situation. In my opinion gitextensions solves this problem nicely and clearly.