I'm not sure if the small differences are all that important. It's not an exact science anyway, so don't stress. It's all an estimate anyway as far as nutrition information.
That said, try looking for food data that is more specific (like "edible portion only" or "weight before cooking"). For things like apples, they'll usually say something like "Large Granny Smith apple", with the assumption that you're not eating the core. But even if you did, or you didn't and they counted the core, it's not going to be a huge deal. It's still just an estimate.