Yes, the Mods and Administrators are aware of this. There is a solution to it for now:
If you're having problems getting a trophy to save in MyTrophies, then you will have to delete the list from your profile and re-add all of the trophies. Go to the MyTrophies page, and click on the red box with the X in it. Disabling on the trophy list won't fix the problem.
Make sure when you delete the list, you use what is in the first image, NOT the second.