Mostly it was laziness, a hell of a lot of the early Amiga stuff was ported from Atari ST code, and the programmers pretty much just made it run on Amiga and did virtually nothing to enhance it.
Sometimes it was because they didn't want the game dropping a frame. A lot of the Bitmap Brothers stuff is done so that the game is supposed to run at a set rate no matter what is on screen. The Bitmaps generally have a lot of stuff going onscreen, which if it ran in 50 frames, would probably slow down and go jerky anytime something big happened onscreen.
Time constraints on a lot of people put them off bothering. If US Gold accepted that the game wasn't going to scroll smoothly, why bother to put the extra effort in? A lot of developers were paid a set price for the game they were converting, so there simply was no incentive to put more effort into it.
And some programmers simply were not very good at all.
Look at the learning curve of David J Broadhurst. Early games like Ghouls n Ghosts to later stuff like Assassin, shows just how bad a programmer he was to start with, and got progressively better.