Board Thread:Online Discussion/@comment-98.250.138.251-20141214225309/@comment-86.130.80.150-20150128185242

From the quest's wiki page -

"After picking up the totem from a chest, if you do not speak to Aela and tell her that you have found the werewolf totem before leaving the cave or dungeon, she will disappear and you will not be able to place the totem in the Underforge"

You'll have to reload a past save i'm afraid if that's what happened. Aela and co have been know to actual go out wandering on their own if that bug above definitely didn't happen you may just have to wait for her to return.