Existing issue https://github.com/EdwardBetts/osm-wikidata/issues/481.

Thanks for pointing that out. I think I did a couple waterways this way before I stopped touching them if they were showing multiple matching ways and no relation in the tool. I'll submit an issue if I can think of a reasonable change. In general the tool does seem to show all the involved ways and the relation, so we might be able to just put this down to user error.