When you press the undo button, it will undo the files with a checkmark. When you right-click and select undo, it will undo the files that were selected (not checked).

I've seen people lose valuable work this way and it's bad, inconsistent UI design. Especially for a function that can not be reversed (in version control software that should prevent the loss of data!).

Maybe, when clicking the undo button, display clearly which files will be reset.

Or remove the undo button entirely, so people use the context menu, which works a lot more as expected.