Maybe you put them into your wagon via the wagon bug.
Curious and compelling hypothesis which I will CONFIRM later, but I strongly suspect it's not the case for me on these occasions. It did occur in dungeons, however, I directly equipped the bow while the swords were still equipped, so they never went into my inventory at all. I am thinking they didn't go into my wagon, 'cause I've definitely been to an armourer since the -first- time it occurred, and it wasn't in my wagon when I sold all my loot. I haven't checked my wagon/tried to sell to a vendor since this second occurrence..
Thanks for the heads-up about that particular bug, though. I may try to exploit it if I can manage to control the situation, 'cause I spent a long, LOOOONG time in the Wayrest palace dungeons passing up uber loot 'cause I was maxed out on encumbrance.. *D'OH!*