Atlas keeps on chanding maps to towers on the already explored territory

Happened already twice.

I was heading for a map with increased XP within atlas territory that has already been explored before the 0.2, completed the map adjacent to the XP map, opened my atlas to insert a map and voila, instead of a map there was a tower there.
So no XP for me...

The second time it again transformed a map into a tower, on my way to another XP map.

How can this happen? How I am supposed to plan atlas exploration, put effort into it when right before my actual goal the map is changed?