The popular pages bot doesn't work fine with taskforces and sub-wikiprojects in some cases. See:
Some projects like https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Military_history/African_military_history_task_force/Popular_pages work. This is because of discrepancies with "project titles" i.e. assessment keywords. The best solution seems to be just to go in and manually fix the "Name" fields in https://en.wikipedia.org/wiki/User:Community_Tech_bot/Popular_pages_config.json to match up with the right project title in page-assessments database. This work can't be done by a bot because it isn't intelligent enough to tell what project likely maps to which title/keyword.