Door leaving gap in wall

Was building a fortress wall. Placed some doors wrong and used the undo button
Steps to reproduce:

  1. build a wall with free standing walls
  2. place a wooden door
    3)use the undo button to remove above step

Expected Results:
door gone
Actual Results:
door gone leaving a hole in the wall
The hole it self is not a big issue, but repairing is, seeing i cannot seem to remove a single wall from a greater construction. And filling the hole with slabs prevents me from replacing a door there.

Version Number and Mods in use:
release 549, debugtools, cafemod
System Information:

It used to be that messing around with the wall settings afterwards would fix this. Does it help or not?

you can only fill it up with slabs but no more doors or windows will go in