when I try to craft red science pack for example. it requires 1 coper plate and 1 iron gear wheel. and the total raw is 2 Iron ore 1 copper ore
when I try to craft the red science pack haveing 2 iron ore and 1 copper ore it should queue up:
1 copper plate, 2 iron plates, 1 Iron gear wheel, and the red science pack.
But the only thing that happens is: it says "not enough ingredients", even though I have more than a stack of iron ore and more than a stack of copper ore. I should be able to craft at least 25 red science packs.
The only way I can craft a red science pack is to manually queue up all the prerequisite items.

As I said in one of the other threads: check what other mods modify the recipes for the prerequisites.

This mod only allows the character to craft the items. This mod does nothing special for queuing up prerequisites. More so, there is nothing it can do - this is part of the core game.

Something that I have seen, that potentially explains what you are experiencing, is if another mod modifies the recipes for the prerequisites in certain ways then the core game cannot determine how to craft them. A simple way to check if this is the case is to look at a recipe with prerequisites, look the the total raw. For example look at the recipe for red science packs. If the total raw consists only of iron ore and copper ore then everything should be ok. But if it shows iron gear wheels and iron plates and copper plates - then the the core game cannot determine how to craft those, most likely caused by one of the other mods you are playing with.

there is a conflict with the mod Reverse Factory (https://mods.factorio.com/mod/reverse-factory)
Hand Craft Everything off and Reverse Factory on = works fine
Hand Craft Everything on and Reverse Factory off = works fine
Hand Craft Everything on and Reverse Factory on = does not work
Hand Craft Everything off and Reverse Factory off = works fine

Are you testing with only Hand Craft Everything and Reverse Factory or do you have other mods?

With only these two mods, everything seems to work: https://imgur.com/4Lcgh1f

This will be very hard without info about what mods modify the recipes and/or add alternative recipes.

2 mods? you must have forgotten to install the library that reverse factory uses https://mods.factorio.com/mod/stdlib
and what about the omnimatter_fluid that is required for your mod?

with only 3 mod enabled (4 including base)
hand_craft_everything
reverse-factory
stblib (Factorio Standard Library that is required by reverse-factory)
it doesn't work
with any one of these disabled, it works fine.

Reverse Factory adds "reverse" recipes for everything. These recipes confuse the core/base game because now there is more than one way to craft most of the items.
Take for example Iron Gear Wheels. They could be made from Iron Plates or by crafting the "reverse crafting" recipe for Engine Unit, Belts, Inserters (or anything that normally takes Iron Gear Wheels as input). The core/base game sees the multiple recipes and either chooses the wrong one or just gives up. This is known behavior.

You can circumvent this by unchecking the "Other recipes" (setting it back to the default false). If you have it set to true, as stated in the description, it will make Hand Craft Everything enable the player character to craft "recipes from non vanilla categories" in this case the hidden category in which "Reverse Factory" has its recipes.

This may not give the desired results for all combination of mods, but this is normal for modding. The only possible thing I could do is to explicitly skip the recipe category of "Reverse Factory" and other mods. But that can get problematic and complicated, so it will not be happening soon.

could you add the option to exclude recipes from certain mods? like a blacklist config file or something where I would put the name of a mod that I have in that file and when it starts up and adds all the recipes that it can find except the ones from the mods in the blacklist config file.