Flags and buildings are unrelated and do not have (or affect) any limits.
Resource stations (e.g. Recruitment Beacons) do count toward the limit though.
No harm done; I assumed that a manual review would clear everything up, but wanted to make sure that would happen ASAP, as I am only out of my home area until Friday morning, so I need every check-in I can get.
Thanks for your time, and the quick response.
Now to get back to making my 2nd, and final, new base for this trip.