Hi,
Unfortunately, openLCA technically allows what you did. I guess you did not participate in openLCA training or read the manual. A process has a reference (product) flow in the output and a waste treatment (waste) flow in the input. If you follow that logic, you get the same impacts.
I think I recreated what you did, by adding the waste flow as reference, but still having the product flow there and choosing it as the reference flow for the product system. This leads indeed to weird results. But it makes no sense to model this way.
Best