I don't know when, how, or why it happens, and yes my action bar is locked (and the abilities are not bound to items or levels granted through items), but every so often I'll get into combat on one of my characters, to get a suspicious feeling that I'm missing an ability.
I'll look at the action bar, find a missing ability, and then have to spend a little while rummaging around to pull it out put it back on.
It's not the end of the world, but I've probably had it happen 4-5 times in the last few hours alone, it's kinda weird.
I would have posted this in the bug/feedback other post, but it's labeled for Early Access, so I'm unsure if it's being monitored anymore.
Thanks!