this is what I see when I hover over the broken drawer, I cannot take out items after that happens and also usually when that happens I get a serious lag as if I was on a server and had over 9 thousand ping, which persists when I try to save the world and in the end I have to close the minecraft using task manager, when I get back to the world one of the drawers, which turns out it is random one each time, will be broken like that, even if it's vanilla item like rotten flesh. The way I fill them up is using a mod called pretty pipes and I use them for mob spawner items. Also if I did something wrong in this issue report please do point it out it's my first time using github to report one.
Edit: forgot to add, I only added one emerald upgrade and void upgrade to these drawers.

I found a way around it but it seems that void uprades are the problem, as soon as one drawers hits it's capacity limit and void upgrade starts working it breaks like that, my way is just letting it fill up without void upgrades and sending rest to a trash can

I've had this problem, too, but for me it seemed to be an issue with Pretty Pipes, not the void upgrade itself. When I switched to Elite Logistical Transporters, the problem did not show up again. A little expensive and step extensive, but far more stable.

I've never had good experiences with Pretty Pipes. The idea is there, but the upgrades just seem really buggy and items seem to sometimes float in the pipes forever, but get deleted when you break the pipes.

If you want your wither skull fragments back, try piping in some fragments with a Mekanism Logistical Transporter. It brought my charcoal back.