Bugged Waystones

I'm writing to let you know of an issue. I just got to endgame and completed my first corrupted Nexus. The original waystone that I used was bugged, causing one rare monster to spawn outside of the boundaries of the map. Due to this, I had to reset the instance by using a new waystone, because I couldn't complete it. When completing the new one, I did not receive Atlas passive skill points. :/ I still have not found another corrupted Nexus and I don't have points. If you are not aware of this, can you please take a look? I'd really appreciate it, since I'd like to get my endgame points.
I've noticed that this doesn't always occur but seems to only happen on Waystones that I've modified myself. The enemies will sometimes spawn outside of the map or be stuck in walls. Since you have to consume the waystone to open the map, you cannot open a new instance to correct this.