Hi Robin,
I would not consider this a bug-the system is working as designed.
When we updated the merge process, many more features within a merge became editable. You can choose a birth date from either profile, or change it altogether, you can use a birth place but update it to be a full name rather than an abbreviation. The same goes with parents. Instead of automatically putting parents into the column of saved items for a merge, you need to manually choose whether to save them. Plenty of fictional parents have been imported in merges with the old system. There are issues with either process.
The thing with this is, it comes down to slowing down when doing a merge and looking over that last column before saving. Whether the parents are auto-populated or not, there's a lot of information that needs to be verified before the save button is pushed. I helped test the updates, and I noticed exactly what you guys have, but found I appreciated it. I just needed to move from doing things at one speed and rhythm to a slower, more methodical one. This lines up with editing the biography, as well. It took more time to complete the merge, but I was happier with it once it was completed. The bottom line? Check that final column every single merge, before saving. Whether the parents are put there automatically or not, they aren't lost forever, either. They can be reattached. Again, it's important to pay attention to the data coming in and act accordingly.
Now, all that said, if this is an issue for a large number of members, we can add it to our future updates for the merge process to change it back. I guess I prefer to update my own work process to accommodate the changes and get improvements elsewhere, though.