Can confirm of this bug that affects me in a similar way. I have 3 sub-tags on the tag #priority : #priority/low #priority/medium #priority/high . When I query something like task-todo:"" -tag:priority/low (so, only medium and high priority), it only shows the medium priority. Same with other combinations of task-todo.
Using Obsidian 0.12.19 on Windows 10.