Maps not completing when defeating boss / full clearing

I just ran 1 citadel and 1 normal map and both of my maps have counted as incomplete (the citadel now shows as failed, red icon) because I loaded a new map node to test this. I full cleared both maps and killed both bosses. The citadel boss icon did not disappear, and I was unable to waypoint out of the other map that had a normal boss. I had to walk out of the boss arena before I could use the portal. Both are not allowing me to progress past the nodes and in the case of the citadel I cannot retry that map and it's at a very important choke point to cross a river for me, so there is no real way around it. In both cases it still says that 1 monster remains in the maps but it said that before I killed the bosses also (yes I checked before I fought them in both cases).