I finally found the time to create a test design that reproduces the issue. You can find it here: https://a360.co/4a5HE82

In the manufacturing model of this design you can find a broken junction. It was used to place the fixture under the stock component that wraps the part.
However, at the moment of creation, by mistake (intentionally in this case, as it is part of reproducing the issue) both the sketch and body for stock were created in the root component, outside Stock. So I guess the joint was initially created between fixture and root component? (I did not pay attention to this at the time).
I could not move both sketch and body to the stock component (too bad, this should be possible) so to fix the thing I had to delete the body (extrude command). Now I could move the sketch to Stock then extrude a new body from it inside the Stock.
Now stock looks good, but the joint is broken and I cannot select the stock as a target.
Apparently in this case the joint holds reference to a missing component (I would say body but joints to bodies should be illegal) and wants me to select a snap point on it? There is no option for me to remove that missing reference and create a new one.