Jack, inconsistencies will always be inconsistencies and thus undesirable.

I've got quite a few ABC transcriptions of tunes where the writer didn't understand the metre and had to guess - very common with 18th century manuscripts of triple-time hornpipes. In that situation you don't want to try fixing it as you transcribe - you copy exactly what you're seeing and try to interpret it later. (Similarly you never want to spellcheck tune titles as you copy; write them down literally).