Maybe someone who has done more scanning more recently than me can give you a more definitive answer, but I have a vague memory from using my Nikon Coolscan IV with Nikon Scan several years ago that the program has a bad "memory leak" that causes this behavior. (If you aren't using Nikon Scan, then ignore the rest of this post and assume the problem lies elsewhere.) Each time you scan and save an image, the program doesn't remember to free up all the memory it was using for it before you scan the next one, and the memory usage builds up until you've overloaded the computer's memory and bad things occur. There are two solutions to this:
(1) Exit and restart the program every couple of scans (what I did for awhile), or
(2) Buy a third-party program to run the scanner, such as VueScan, that is written by more competent software engineers (what I learned to do after getting annoyed with Nikon Scan once too often).
My experience was with a version of Nikon Scan from something like four or five years ago, though, so I'm not sure exactly how the current version might be different...