I've got an ore patch that has both copper and Uranium. However the excavator refuses to mine copper, I don't want to mine the uranium so no acid is hooked up.
Is this a bug or am I missing something?

Sadly this is vanilla. The Mining drill (in this case the bucket wheel excavator) "randomly" chooses the ore patch it wants to mine. And it doesn't let go of it. So once it hits the uranium it will refuse to mine copper until sulfuric acid is supplied. The only way to prevent this is to relocate the drill.