I had a similar thing happen a couple of weekends ago changing the brake pads on my daughter's UTV. I go to assemble everything back up and the outer brake pad was jamb up so tight against the rotor I couldn't turn it. Like you I removed it multiple times and couldn't figure out why it wouldn't go all the way back on. I ended using a deep socket and tapped the bearing to make sure it was all the way in. Put it all back together and everything was good.
How the inner bearing moved in the first place I have no clue. It's pretty snug in there.