This bug is of particular note to me, since it was one that I discovered back when the Dragon Ruins was the furthest you could go in the game. I reported it then, and it obviously hasn’t been fixed since.
If, after Audrey floods Kepler City but before you enter Maelstrom 9 to defeat her, you leave Kepler City and then use a PikaTaxi to return to it, Kepler City will no longer be flooded. You can’t fight Anastasia, as the Gym is empty, but you can continue onto Route 11 and use your newly acquired Scuba Gear to head straight for Nasca Town without fighting Anastasia. If you leave towards Maelstrom 9 and then re-enter, the town will be flooded again.
In addition, as another oddity, if you enter the Kepler City Pokemon Center during the flood, you will wind up in the old version of the Pokemon Centers, with a clothing store downstairs and a PokeMart upstairs. Entering your secret base through the bookcases and then exiting will bug you into the upstairs of the old Pokemon Center and cause you to be stuck in a wall, unable to move.
These are all very serious, as one allows you to skip 3 important fights and the other could potentially render your game unplayable. Looking at previous threads on the subject show that this has been reported several times, but nothing has been done about it. Is there any chance a future update will resolve this issue?