I suspect the culprit may be my mod (quality control). I'm still investigating, but here's what I think happened:
Quality control upgraded a hidden entity (one of the sub-entities of a mini loader); by doing that it would have probably messed up references in miniloaders ml_entity.inserters table.
This could cause the problem when miniloader tries to access inserter.direction on line 588, it would fail with "LuaEntity was invalid"
Sorry Xaal, I hate that this broke a save in a bad way that would be hard to recover from. It was surprise to me that hidden/compound entities exist.
I'm working on a migration in quality control to look for and fix the broken entities, along with the change to prevent quality control from touching miniloader entities specifically.
Investigating this problem made me aware of the destructible flag on entities, and the selectable_in_game property on prototypes; which will be good generic ways to prevent issues like this re-occurring from my mod.
This all assumes I understand what happened correctly.