create a file and write a line with trailing spaces into it. Now keep the cursor at the end of that file and press "Ctrl+S - the trailing space is still visible as a greyed dot. Move the cursor to another arbitrary position and press Ctrl-S - now the trailing space went away. Reproducible: Always
Please see bug #310712 for a reasoning for this behavior. We're not claiming that this is a good default, though, so I'd be fine with changing that for the Kate 5 version. *** This bug has been marked as a duplicate of bug 310712 ***