When you kill enough enemies at the same time, especially in one spot, the explosion graphic (which can look almost like a full filled in circle with enough enemies) and the lingering plus counts can severely slow down the game. It would be awesome if the game would limit the number of these shown at one time to a sane amount and make the gameplay smoother for those of us who like to make four badass mega mega towers and advance a few hundred waves on survival. ;)
BTW, wave 666 was cursed. Pure evil.
There is a noticeable slow down as you pass 12800 meters, and every time you pass another mark it takes longer and longer and longer for the game to respond. I assume there's a bonus when you hit these marks, and that bonus starts to take forever to be applied.