This might be a similar issue to the one I encountered when using another of these extensions (timestampable), namely: that the default change tracking policy used in doctrine (it tries to auto detect changes) sometimes marks entities as dirty, when they are not (for me this was happening when my entity contained a datetime object, which is understandable given that this is an object which needs to be constructed when pulling it from the database). This isn't a bug or anything - it's expected behaviour and there are a few ways around it.
Might be worth trying to implement an alternative change tracking policy on the entities you want to log and seeing if that fixes things - I would guess that this behaviour (logging) doesn't kick in unless the entity state is dirty, which you can avoid by implementing change tracking yourself manually:
Don't forget to update your entity:
YourBundle\Entity\YourThing:
type: entity
table: some_table
changeTrackingPolicy: NOTIFY
See this thread:
https://github.com/Atlantic18/DoctrineExtensions/issues/333#issuecomment-16738878