I've run into this a few times, but finally managed to come up with a reproducible case. Sometimes when deleting (or moving) a feature preceding a Boolean cut, the Boolean result is wrong, but FreeCAD ...
Currently (FreeCAD 1.1dev), boolean properties have two states in the properties panel. Checked checkbox and Yes text or unchecked checkbox and No text. This can be confusing, as the text seems to be ...