Inconsistent 'clean up' behaviour

Just noticed that >cmd+shift+k< does not always work.

Three examples in picture:

1. quickly drawn alkyne - cleans up as expected

2. join two ends of a chain to make cyclobutane and get a stretched bond. This will not clean up - >cmd+shift+k< does nothing

3. if I draw a distorted cyclobutane, the structure cleans up fine.

Not sure what about joining bonds has killed the clean up