Not sure exactly when this happened, but a number of links from the docs (https://xtools.readthedocs.io/en/stable/api/index.html) are busted. I think it's only project and user, not page, tools that are affected, including: automated tools, admin groups, admin stats, automated editcount, nonautomated edits, category editcount. The quote links don't work either.
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Same issue as T203339, I assume. Somehow some of the production cache files went missing. This was fixed by force-clearing the cache again (which in turn regenerates all those files). I could have sworn I checked all the APIs after T203339, hopefully I didn't -- meaning it is a one-off issue and not persistent.
My theory is the cache wasn't completely cleared when we updated all our dependencies in the last release, effectively a "bad deploy". Normally the Symfony console command works, which is ran automatically, but it seems with major updates you need to manually delete the cache directories. We'll be making other major updates soon (T188699), so we'll have to be sure to do the same after deployment.
Thanks for the report!