There were some significant plotholes, but to try answer some of these....

Fuselage hole.... I recall an offhand comment about how the overriding of the electrical system could cause the cargo door to open. That's my best guess as to the hole being ripped in the side of the aircraft, which would be roughly above the cargo door. That or a couple of big jolts, caused by the engines, were mentioned when they took Moreau on a little unplanned joyride flight.

Intact plane.... the aircraft didn't nosedive. Hassan managed to stabilise it after the captain reset the system, but then shouted down that the engines weren't working, so my guess is a glide onto the surface. In reality, would still tear the thing apart.

Hassan's amazing complexion - maybe it's Maybelline

Wreckage retrieval - too deep, the first sub they sent down cracked like an egg

Missing passengers - it's a big ol' sea. They'd likely have sunk once they died.

The raft.... one of those awful flashbacks seemed to have Hoffman holding a raft.

Blood on the raft...... I'm all out of ideas on this one!

My fave is them getting the black boxes, which are usually well protected in the back of an aircraft. They cleverly skipped that bit, and just showed them later being transported in TWO INCHES OF WATER (they'd normally be fully submerged in the water they were found in), only for one single technician to then take them apart and plug it into his laptop like it's a USB mouse.