Seems there's a bit of cross mod funk with Containment Jars and mods like Industrial Foregoing and Occultism that have an item to right-click pick up mobs.

Industrial Foregoing: Mob Imprisonment Tool
Occultism: Soul Gem

When either of these are used on a Containment Jar with a mob that doesn't have other right click actions (skeleton, for example), the item gets a copy of the mob in the jar, but doesn't remove the mob from the jar. Breaking and re-placing the Containment Jar allows another mob to be extracted in the same way.

EnigmaticaModpacks/Enigmatica9#294

Perhaps a tag or other config could be added that prevents certain items from being used? These two items could be added by default as well.