I think I have also encountered this bug. Numerous Ascension Crystals were all over the map. Furthermore, when I built starbases on the Ascension Crystals, the Ascension victory number count remained at zero.(In other words, having starbases on the Crystals did not do anything.) On the foreign relations screen, the other races did not show any "You are trying to ascend" negative signs.
In two previous games that I played, the ascension crystals were working like they should. There were only five of them in the galaxy, the Ascension victory progress count increased when I had starbases on the crystals, and I received the appropriate negative relation sign from the other races. I will submit an error report about this bug.
EDIT:
When I reloaded my game, all of the fake Ascension Crystals disappeared, and the starbases that I had built on the fake Ascension Crystals had no resources in the middle. Until this bug is officially fixed, you apparently can get rid of any fake Ascension Crystals by saving and reloading your game. This probably means that this bug cannot be reproduced by a saved game (making Stardock's job more difficult). If you get this bug and find that the error persists after you save and reload your game, put your game save in a zipped folder and send it in an email to:
gc2bugs@stardock.com