When our heroes wake up in their submerged St.Anne, Ash noticed fishes roaming around through a glass window nearby. This kind of window cannot sustain such water pressure under water that deep.
When Geodude is out, it weighs down the ship a lot, yet when Brock calls out Onix to make a staircase, nothing seems to happen, despite the fact that Onix is a lot heavier than Geodude.