http://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=852802967

http://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=852803212

http://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=852803521

Only actual companions are listed in autoloot, it's intended otherwise you could gear up kidnapped girls and have them reappear the next time the quest gets offered.
I'm assuming you recruited the wife as companion? The first time you recruit any hero script_dplmc_save_civilian_clothing gets called which duplicates their current gear. This is a one-time only thing, and your wife should have received equipment to that effect to overwrite the dress she was wearing.

I've tried giving stuff to her before, but it deletes whatever I give her and she keeps whatever she was wearing.

yeah it still thinks she's a civilian so it restores those items from before you recruited her. Upload your savegame somewhere so I can take a look please.

https://mega.nz/#!a10yiIqT!h75b_ZcrFoCl2ihAA2KjnODEjUDSYQqMPEyJZtRi1FU
Here you go.
The issue may be fixed in the 1.171 update, but I can't test it because my wife isn't of the right personality to join my party.

Alright, I'll take a look and see if I can fix this