You can now only do online 90 day reporting from 15 days to 7 days before the due date. If you miss that window you have to report in person hence your rejection.
Just as there are no numbers on arrivals there is no numerical limit on the maximum number of days you can stay in a calendar year or rolling year. It's entirely at the discretion of the Immigration Officer.
There is no limit on arrivals but what will be a red flag to the Immigration Officer holding your passport is the amount of time you spend in Thailand on tourism entry stamps