The --prune option is useful for telling mkid not to look into certain places, such as .git directories and whatnot.

I have a list of such exclusions and put them into a script which calls mkid.

Not all to-be-excluded items exist in all directories. But mkid complains about all the --prune items that do not exist.

If I wish that a tool not process object X, the tool should probably not complain that it would like to ignore X, but X doesn't exist!

(If there is a solid rationale for --prune to diagnose, and continue to do so, please consider adding --prune-silent which doesn't.)

Other tools have similar options which don't diagnose nonexistence.  I pass the same list of exclusions to ctags (via its similar --exclude) option and it doesn't complain.

GNU tar's --exclude=PATTERN certainly doesn't complain that nothing matches PATTERN. GNU diff's --exlude=PATTERN doesn't complain, either.