What Should I Do If I Missed My 90-Day Reporting Deadline in Thailand?

you aren't gonna get it to work either by the application OR by the web-based online portal trying to do it AFTER your actual due date.

SO you either slog to the immigration office and file a 90 day report in person this week (which is a good choice because all the offices are near empty now) OR you take the amnesty on filing 90 day reporting, don't file and wait for the news from immigrations on what people who took the amnesty have to do when the amnesty runs out.

For the online reporting to work you need to file it from 15 days before down until the date it's due.

Seems like you were either trying too early OR too late.

AND

there seems to be a discrepancy with your current extension of stay stamp in the data base not matching what your actual stamp shows in your passport. That's why you got that error prompt.

You can file a 90 day report IN PERSON from 15 days before down until 7 days AFTER your actual due date without any penalty,

I'd say go file the 90 day report tomorrow, OR Thursday or Friday immigrations is closed today and Wednesday).

We are advising people on long term extensions to just go file their 90 day report like always

okay, you can't use the application IF you're trying to file a 90 day report AFTER it's due.