My armory is showing 13950 achievement points, but in game I have a little over 16k. Specifically armory is not showing any pet battle achieves. There may be others not showing up but I didn't do a thorough review. Not a big deal just wanted to report it!
Website issues - including the Armory - should be reported on the Website Bug Reports forum. A separate team handles things outside the game to the one which handles things within the game.