NO LONGER RELEVANT. The issue was resolved in FNEI. Below is the explanation of a historical issue that NO LONGER EXISTS.
If you played with Pyanodon's mods (Coal Processing, Fusion Energy, High Tech) and used FNEI to deal with the complexity you may have noticed that some of the recipes were missing from FNEI. I think Ralesia is the one you'd run into the earliest, but refer to this table of the all the missing recipes I found.
The issue here is when FNEI checks what machines can make a recipe it involves two things: recipe category and ingredient count. The ingredient count doesn't come up much, it's only relevance in vanilla is when assembler 1 can only make recipes with up to 2 ingredients, and assembler 2 with up to 4 which creates some restrictions. It doesn't come up so much, that it's not even widely known that fluid ingredients are not counted when applying the ingredient count restriction. FNEI doesn't know, and doesn't apply this logic when figuring out what machines can make what, and since PyMods is all about pushing the limits on how many ingredients you can cram into a recipe, FNEI is fooled sometimes when a recipe appears to have more ingredients than its machine can accept, but it's actually fine because some of the ingredients are fluid.
A proper fix for this would be to change FNEI logic to disregard fluid ingredients in the same way as the game does, but the logic is buried deep within the code with no easy way to inject an outside fix. So instead this fix increases ingredient count of relevant machines to make them eligible by FNEI's rules. This should have no impact on gameplay or balance as for the most part PyMods have a single machine for every category of recipes (great design, btw, I hate the unending tiers of everything found in some other mods), the ingredient count is just a meaningless number.
To report an issue, a suggestion, etc, try to do it via GitHub is at all possible, as the mod portal's discussion doesn't have notifications.