Door leaving gap in wall

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1

Summary:
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
Notes:
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.
Attachments:

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

2

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

3

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