There is rumor that if you un-equip via double click, sometimes they eat each other.
I have never tried it but... well... that might be why. Check your lv/exps, see if any randomly grew

Well, at least now you know how/why it happened.

It shouldn't and is certainly a bug but...

The mods insist that the lack of confirmation bit is false, but like I said, i have never tested it so I won't know.

Someone should probably record a video of this stuff to prove whether a confirmation box ever pop up when stuff gets merged this way. Given that this isn't happening to only one or two player, I seriously doubt everything is working the way they should and the mods should think twice before blaming it on player inattention.