I have the same problem: Champion subjugator and Rare sand dweller are not checked in the box when i kill them.
Also problems with some champions and rarte versions of: skeletal archer, skeletal sentry, skeletal raider, skeletal marauder, dust imp, fallen cur, plague swarm, armored destroyer, armaddon, and the never-seen-before MALLET LORD champion and rare version.
So Blizzard, you have make us to pay you 60 euros (in europe) to play your BETA GAME. And instead fixing the bugs that people need to be solved to complete the achievements, you are implementing only incoming-money-features-for-you like that stupid RMAH.
So, next patch, instead of coming with all this stealing-money-codicious-features, please fix the bug that make this game interesting to be played. Please fix the boss spawning rate for complete ther achievements, PLEASE FIX THE DROP RATE OF THE "BATTLEFIELD REPORTS" LORE BOOK FOR THE BOOK QUEST ACHIEVEMENT.
If you dont fix that bugs, the game will not be interesting to be played, and people will leave the game, and noone will be interested to buy REAL MONEY ITEMS in the AH, for a game that cannot be completed (in his achievement aspect).