Most of these were not found by me, and were posted on your discord, I'm just reposting them here, since I'm guessing you haven't seen them on there.

Bronze plates, copper tungsten and tinned cable, can't accept prod modules. (Found by Baisius),
Electric Foundry requires production science packs but not production science to be researched. (Found by Baisius),
Mainboards including the SE holmium recipe and CPU's don't accept prod modules (Found by me),
Hydrogen Chloride from sulfuric acid doesn't accept prod (Found by Sidd),
The noble metals catalysts can't accept prod. (Not sure if this one is intended or not. found by me),

I may have missed one or two so you may wanna check your discord just in case.

I know this post is 7 months old but seeing as you've returned and there is one other large issue that is not in this list thought I would give it a bump instead of making an entire new post

Issue with Noble metals the foundry refactory recipes are quite messed up while I can't remember the exact math the gold recipe too way more gold ore than it should've.

Also good to see you back.