This pet http://beastkeeper.com/pet/302799 should be GP2 because both parents are lvl 50 GP1s but it's only showing up as a GP1.

Were both of this pet's parents level 50 at the moment of conception or did one or both of them levelled after?

The mother has been lvl 50 for quite some time and unless the father leveled up in the 5 or so minutes between her visit to the fertility shrine and my checking him out to see what kind of parent he was, then yes, he too was lvl 50 at the time of conception.

Hmm, Angel will have ot confirm this, but I'm pretty sure the genetic information for a stallion is taken from the time he visits the shrine, not when he is used by someone else's shrine visit. And this can take quite some time. One of my stallions visited the shrine a long time ago, but the other day when i went exploring with him again and encountered a fertility shrine, it said that he had his info already stored in the system. 

So, long story short, my guess is, the father of your foal was probably not level 50 when he visited the shrine, by the time when your mare got studded by the shrine he was, but the game used his old info of when he wasn't.

If the pet was conceived through Fertility Shrine, then Timain is right. Fertility Shrine stores genetic data of male pet at the moment of visit. It doesn't have any connection with this pet after visit. The father of the pet in question was level 4 when visiting the Shrine.

That sucks. I wish I had known that when the shrines first came out or I wouldn't have donated the genetics of my males under 50. Time for my next suggestion, I guess.