What options do I have for 90-day reporting if my online application was rejected?

Two weeks before report date to one week before report date and it usually goes through with no issues.

Yes, we have recently been getting reports same as your case, rejected if you applied for a 90-day report online less than 7 days BEFORE the due date

You have to slog to the local immigration office where your TM30 is registered to do it in person if you don't want to get a fine of 2,000 baht for lack of a 90-day report. If you are in Bangkok with your TM30 being registered in Bangkok, you go to Chaengwattana within the next week as the window of reporting in person is until 7 days after the due date including holidays.

Btw, the online reporting window has not been 7 days after, was only until the due date.