I've completed Both counterweights and big ben twice, going through the third time helping friends and through everything it has not counted any of the clockworks towards my golem badges. I'm still locked at 96 golems defeated.
I checked by killing clockworks elsewhere in the game and they didn't count towards the badge.
Hmm I'm not sure I know the answer to this. Let me ask our Design wizards. Update! You're correct, and this is a bug. I've made sure it's on the list to be fixed, but you can always duel against the Desert Golems in the Palace of Fire. They count as Golems, Giants and Elementals!
