There seems to be an issue with Refined storage sometimes not consuming enough resources when crafting in ATM 9 version 0.2.34. I noticed this after our server upgraded from 0.2.21 to 0.2.34.

Setup where I first noticed the issue: I have all my essence in a Netherite chest with stack upgrades for bulk storage and connected to my Refined Storage network via an External Storage. When manually crafting the essence into items through my Crafting Grid it seems to be giving me more resources than it should. For example, I had 247 Diamond Essence. I put in the pattern to turn 9 essence into a single diamond and shift clicked. It produced 27 diamonds, but then I still had 123 essence in my network.

I've tried various combinations and can't quite pin down the issue, it seems inconsistent. Sometimes it happens with items that aren't Mystical Agriculture if I store them in the Netherite chest, sometimes it happens with Mystical Agriculture items stored directly in my Refined Storage drives, sometimes Mystical Agriculture items stored in the Netherite Chest work fine.

I was just having the same issue on update 0.2.34 with creating the master infusion crystal. I even pulled all the previous crystals out of RF and was still able to make endless crystals.

Doing a bit more testing, the easiest way to replicate the issue is combining an RS Network with External Storage to a Sophisticated Chest that contains a stack upgrade. I was able to reproduce this reliably in a fresh single player world.