There's already handling for trying to add nonsense adducts that would remove more atoms than are present, but even that needs improvement - it turns the textbox contents red and refuses to commit the change, but doesn't say why. Probably a tooltip with the reason is the way to go there and in the molecule setup as well.

Skyline issues have moved to GitHub Issues at https://github.com/ProteoWizard/pwiz/issues
Issues will be ported as necessary for active work.