This always happens when I can apple slices. After 24 hours (to be sure that they're sealed) I either turn them upside down or give them a quick shake.
I've had that happen with tomatoes. Was it a wide opening...That often happens with wide openings. I choose narrow for that reason....Also after about a week, turn over and sit on tops and they should settle when they turn over. Sounds delish!
I figure it is like tomatoes I raw pack mine and cram them in the jar as tight as I can yet when they get done settling they are always up from the bottom a little bit.