I guess something's wrong with the SQL queries because, for example, it lists astwiki with 1 user in the 'checkuser' group, which at this moment ain't true (the same for several others).
https://github.com/wikimedia/labs-tools-stewardbots/commit/261fda1c58556c21e479ca6dab1a7a4abdc09672 didn't break the tool (that's a step forward), but it's still displaying incorrect data. For example, search for projects with 1 CheckUser and you'll see that in most of them, that's not true. Either the MySQL query is broken or badly formatted, so it give us wrong results.
https://phabricator.wikimedia.org/diffusion/TSTW/browse/master/hat-web-tool/projects.php does not take into count ug_expiry from user_groups, so it's potentially listing a lot of outdated data.