Revealing mistake: When Chekov and Terrell are walking on Ceti Alpha V watch as they get to the ridge overlooking the Botany Bay. Each of them cast two very distinct shadows, indicating two separate light sources. The planet only has one sun. (00:15:05)
Revealing mistake: When the Enterprise is leaving space dock, look at the right (starboard) side of the ship. You can see the shape of the mounting arm the model was mounted on, even though it was blacked out to look like space, and it also blocked out the bottom of the dock. The footage was reused from Star Trek: The Motion Picture.
Revealing mistake: Near the end when Khan says "For hate's sake, I spit my last breath at thee", if you look near the bridge of his nose you can see the prosthetic of his "wounds" is coming loose.
Revealing mistake: When Chekhov and Terrell see the Ceti Eels moving around in the tank for the first time, it's obvious that it's not sand in the tank. As the creatures move underneath, all the 'grains' move in unison, and not a single grain of sand is disturbed nor do they tumble over one another.
Revealing mistake: On the Regula station, when Kirk, Saavik and McCoy set phasers to stun, McCoy is squeezing the trigger on his as the emitter light is lit. He is still holding it down as he turns to walk off.
Revealing mistake: After crippling the Enterprise, the Reliant comes around again. As it does, the star field behind it can be seen through the black area of the inside of the nacelle.
Chosen answer: I imagine there was a memorial service for everyone killed. Starfleet's policy on corpses is probably to return them to Starfleet HQ where their families can collect them for whatever services or ceremonies they want unless the crewman had left instructions specifying otherwise. There's no telling why Kirk sent Spock's body to Genesis. Based on Sarek's reactions in ST3 he almost certainly went against Spock's wishes, unless of course, Spock left no recorded instructions and Kirk did what he thought would please Spock based on his being highest ranking officer and Spock's closest friend. It also seems very out of character for Spock to just assume that whoever he transferred his katra to would be able to handle it and carry out his wishes (McCoy certainly couldn't!). Ultimately it seems we have to chalk it up to a plot device to base the sequel on.
Grumpy Scot
According to the novelization, Kirk's intentions were to send Spock's remains into the Genesis sun. Lieutenant Saavik altered the trajectory of the torpedo beforehand, due to Spock's desire to see the Genesis effect for himself. The torpedo casing was expected to incinerate when entering the atmosphere. As pointed out by David Marcus in STIII when the pod was detected on the scanners, the gravitational fields were in flux at the time, and the pod had obviously soft-landed on the surface.