Have a look at the pickup's legs and see how straight they are - if they're the "long" legs, they sometimes get bent slightly in or out.
Even if they are already straight, you can probably bend the legs slightly until they line up - humbuckers are pretty standard sizes so it shouldn't need much adjustment. Be very careful, though, so they don't snap!
Edit: I'm assuming they're sitting in mounting rings. If they're screwed directly to the body, you might need to plug the existing holes and re-drill them.