Same thing happened to me. Did you find a fix yet?
Yeah, when you enter the save file start spamming the ~TAB~ button (or the in game menu where it shows yout ~bag~ and ~pokemon~), it puts you above ground, if it doesnt work for the first time close the game without saving and try again until it puts you back on top, then save when it works to not bug again.
Warning: i had some minor issues after correcting it, but nothing big just visual bugs