I added 4x diamond chipset, red wire, blue wire, green wire, and yellow wire to the assembly table to create four diamond and gates. One was built and consumed 4 red wire but no others.

I couldn't reproduce that error. Can't you give us any more information to help other people reproduce it?
BC version, forge version, crash reports if any.

I also see this error. It's consistent. No crash reports. Version info:

Minecraft 1.5.2
BuildCraft-A-3.7.2.jar
Forge: Forge Mod Loader version 5.2.23.737

This happens with pretty much any gate. They seem to prefer to use red pipe wire, but this could be random. They'll also eat two red pipe instead of whatever other pipe. Makes autocrafting with these unpossible!

Not easy for us to update, or I'd try with the latest version, just to make sure. Sorry about that.

Reproduction steps:

3 red wire
2 blue wire
1 gold chipset

Enable the gold and gate recipe.

Expected result:

1 gold and gate, 1 blue wire, 2 red wire

Received result:

1 gold and gate, 2 blue pipe wire, 1 red wire

It's almost like isCraftingEquivalent is returning true, but I don't see a way it would do that. Since the recipe doesn't just take an extra wire, that would imply the second part of the recipe is being fulfilled by the red wire, which shouldn't be possible unless the equivalency check returns true. Since that's just an item id comparison and these aren't mapped using ore dictionary... ?

The other possibility, that we're getting an extra deduction from the stack, would just result in extra material being removed, which isn't happening here. 2 pipe wires == gate.

I tried to track this down, but I see no obvious bugs or recent commits to fix anything that would cause this issue. Maybe they're older ?

I checked the ids in my config and the two pipewires have different ids, so that's a dead end.