What do you mean the wheels don't sit right?
Most OE wheels are hub centric. Most aftermarket wheels are lug centric. If the aftermarket wheels with their larger center bore than the OE wheels don't have the proper lug nuts to center the wheel on the studs, it can result in the wheel not being centered with the hub, which could lead to working the lugnuts loose, as the wheel shifts on the hub. Not to mention the poor ride which would result.
Yes, it does sound like they've got it in for you. I'd be seriously looking for new opportunities, before they claim they let you go for cause.