Nnnnh - there was a similar stuff-up when Air Force One circled lower Manhattan at low altitude a few years back for a photo op.
Supposedly the communications P&P were improved after that, but I guess not entirely.
Seems to be a bureaucracy-to-bureaucracy foul-up, not the pilots or ATC (above their level, and they seem to have done their jobs just fine). Capitol Police were just not on the "need to know" list for some reason.