If I autoinsert soybeans into the presser, the output slots get filled with soybeans, too
and there is no JEI support for your custom machines

1.12.2, latest of everything

EDIT: JEI fixed with this: https://minecraft.curseforge.com/projects/just-enough-harvestcraft

There are also no item tooltips in your machines.
Add this to your clientGui Class

@Override
public void drawScreen(int mouseX, int mouseY, float partialTicks) {
    super.drawScreen(mouseX, mouseY, partialTicks);
    renderHoveredToolTip(mouseX, mouseY);
}

It may depend on which version of Forge you are using or version of HarvestCraft. I do not have this problem and 1.12.2 everything also, and do not use "JEHC". Soybean in Presser gives me Tofu and SoyMilk.

Minecraft 1.12.2
HarvestCraft 1.12.2a
Forge 1.12.2-14.23.0.2491

It works, yes
but hoppers (for example) insert into all three slots, if they are all empty

JEHC fixes only the recipes in JEI, without this mod, the custom crafting methods aren't shown in JEI

Hoppers and pipes, yes

You mean with hoppers? It is currently messed up in hoppers.

@MatrexsVigil
if you accept PR, I'll fix this and a few other small bugs in the next few days

Can confirm, still happening with mekanism pipes as well, even using a logistical sorter and setting it to only output 64, but fills all 3 slots.

@TimGoll Yes, I accept PR requests.

Fixed in 1.12.2g