Tower completed but map still in progress

The last two towers I completed where not registered by the game.

I completed the towers as usual and used a "The Grand Project" tablet. The map itself says "Map Completed", but on the Atlas it is "Map in Progress".

Did you activate the beacon or just killed the boss?

I activated the beacon both times.

Unlike other attempted maps, things like "Cleansed" are still there and I could use normal tablets again. But not the "The Grand Projekt". So it seems like the tower is now registered as a normal not attempted map.

Maybe that helps fixing it.

Just run another map. This one become completed.

I cleared a couple of other maps between the first tower and the second tower. It did not change the completion of the tower and "The Grand Projekt" still had no effect. I can still run them, they are not completed.