It's not a bug per se, but an exploit available in combination with other mods.
For example, using Mystical agriculture, one can gain experience by upgrading essences, downgrade them, and repeat.
Maybe a config "do not get bonus experience for these recipes" could be a solution, detecting them automatically probably is a nightmare.

Oh, right, those need a secondary item. I'll see what I can do.

It should be detecting them automatically already. What version are you using?

I am using Level Up! 2-1.1.8-1.12 and mysticalagriculture-1.12-1.6.5 .
I tested again with these 2 mods only and it still have the loop.
To reproduce : give yourself a stack of superium essences (blue) and a master crystal, downgrade the essences into 4 stacks of red ones, combine them again with the crystal to make a stack of blue ones.