I've noticed that there are sometimes (large) differences between the reported total CPU usage and a summation of the per-process CPU utilization given by apps like top and wmtop.

As an example: I recently ran a git filter-branch --index-filter on a fairly large repo, with the index-filter command piping git ls-files through a grep filter and into xargs git rm --cached. This took a few minutes to run; while it was going I noticed that both wmtop and top were displaying a high (above 50% on my 2-core machine) total CPU usage, but that neither showed any individual processes which were using a significant amount of CPU time.

Are some processes not shown in the process list? What sorts of processes are these, and is there a way to find out how much CPU time they are using?