Hm, then I'm also clueless how it might be happening. The ways in question is w1052848283 and w1341422886. In the first case, buses will go from "Rua Principal" to "Rua do Chafariz Velho" (some buses will come from one part of "Rua Principal" and others from the other part). On the second one. Buses should go from "Estrada das Ameiras" to "Rua do Chafariz Velho" via Largo do Rio Covão.

P.S.: I've been testing a bit and I think I've found the issue, OSM iD checks seem to be very basic and just check if both ways are in all the relations. In these bus routes, the relation goes from "Rua Principal" to "Rua do Chafariz Velho" but it also goes from "Rua do Chafariz Velho" to "Rua Principal" (other direction) Since both ways of "Rua Principal" is in the relation, it figures it's ok to merge the ways. JOSM on the other hand will give a warning even in such cases.

It's not worth to fix these in particular since i'm preparing a changeset that will fix it together with other bus routes. Regarding OSM iD, there's not much to do as it doesn't warn in these situations and the bus routes don't show up that well. 

In any case, appreciate your time for this discussion and for the added street names.