One thing that bothered me about this movie was the whole "surprise" of finding Khan there.
When the Reliant was dispatched to the Ceti Alpha system, why wouldn't Chekov think "Oh yeah, that's where we dumped Khan!"
Also, the great, mighty StarFleet was completely unaware that a planet in this system exploded? You would think somebody at some time would have noticed....at the very least, Reliant should have detected that the system no longer matched known charts, because...well...a planet exploded and shifted orbits of the others!
Khan remembering Chekov can easily be explained...Chekov appeared off screen as a minor crewman. Khan had access to the ship's records (another brilliant move by Kirk!) so he memorized everyone on board....
But...the whole "planet-exploding-in-the-system-where-Khan-was-left-and-nobody-noticing" is a bit hard to accept.
Not to mention, the wonderful scanners on the Reliant that missed Khan and the rest of the survivors...or having them show up as a minor "fluctuation on one dyno-scanner."
Carolyn Marcus wanted a planet that "was completely dead or the deal's off." Maybe next time send a ship with better scanners?
Oh...and now that I remember, once Chekov figured out where he was, why not call for an immediate beamout instead of going outside to be captured by Khan? Let me guess, the transporters couldn't penetrate the cargo bay!