It sounds like you may have a 'shadow ban' that is Niantics new way to combat bots and scanners.
It appears false positives are rare, but this is not the first report of one I have seen - and I guess we may see more.
I believe you need to contact Niantic support, and try to get it liefted. All reports so far seem to say that it can get lifted but may take a couple of days.
Good luck...I hope this isn't the case for you.
For reference.
https://www.reddit.com/r/TheSilphRoad/comments/6d8p43/has_my_husband_been_shadowbanned_or_is_this_a_bug/?st=j35fl13d&sh=ea691222
EDIT It is also possible to get 'shadow banned' by using 3rd party IV checkers that log in to your account. See the link I provided for more details