I noticed that deduper function causes several weird bugs in recipes, as it removes ingredients that shouldn't be removed.
I manually modified this function to ingore specific recipes:

if string.sub(ings.name,1,string.len("fish-"))~="fish-" and ings.name~="science-pack-gold" and ings.name~="military-science-pack" then
data.raw.recipe[ings.name].ingredients[a] = nil
end

and that fixed those:
-Meat, Bones and Blood from all fish - deduper removed fish from recipes, so those could be generated without anything
-Gold science pack - same thing as previous, removed all science packs from recipe, so it could be generated free
-Military science pack - deduper removed Piercing rounds magazine and Grenade, so it only required Wall.

Also, I noticed that in recipes for generating Meat, Bones and Blood from fish and biters, Bones and Blood are duplicated. so it couldn't be crafted as Steam Assembler could only output one fluid, not two. When I removed this from prototypes\angels-mods\overrides\overrides.lua and left only in prototypes\angels-mods\overrides\overrides-updates.lua it worked properly.

That is the cause of my fish problem! Been digging around trying to figure out what the cause was. Where would that if statement go? It was a bit creepy to have factories that produce body parts with no input.