I gave Aela a nice ebony bow of soultrapping and she wore it at first but then after the next dungeon I noticed she has no filled gems and the ebony is not wielded. She is visually wielding some bow, but whatever it is its not showing up in her inventory so I cant take it away from her. Nothing she has could be even close to ebony. I took away an orcish bow to give her this one. Is there any trick to taking whatever she is using away so she is forced to use the ebony?

You can pickpocket it from her with the right perks I believe. Otherwise you can use the console if you are on PC.

Have you supplied her with arrows too?

:tes:

Followers are supposed to use the best equipment in their inventories, although I think I read somewhere Aela doesn't use the best bow all the time and uses her default one.

Here, listed under bugs:
http://www.uesp.net/wiki/Skyrim:Aela_the_Huntress

Figured a workaround. Took the ebony, told her to leave, then invited her back and gave her the ebony and she equipped it right off.