The stale bot will unhelpfully ask if "this is still an issue" or if something is being waited on for a pull request. You take the time out to reply, so that stale bot keeps the issue open. Repeat this meaningless back and forth, for months as the maintainers ignore the issue or pull request. Eventually lose the will to continue and let the bot close the issue or pull request.
Net outcome: A potential contribution or solution lost.
Stale bot only exists for aesthetic reasons, to keep issue lists clean and to close issues that maintainers don't want to deal with directly by abstracting away the interaction.
More maintainers should understand that it's OK to just ignore an issue but leave it open.
If it's configured with a short timeout and with preventing further comments, I totally agree. That's rally annoying. But maybe there are circumstances where it's actually useful.