What should I do if my 90-day check-in in Thailand was rejected by my agency?

Go to immigration immediately

Do it yourself it's very easy to do

Where are you

Go on government website I use this every time for my 90 day report and never have a problem

Really? You use an Agent to do your 90 day report? Easy to do yourself unless too busy 5555.

So easy to do yourself and costs 0 baht.

That's the joys of helpless people who can't carry out a simple task themselves! 😂

I don't suppose your kind agent will be refunding you 2000B for your fine?

It sounds like your agency was filing online for you, and that what they filed was rejected. Most likely due to international travel or a TM30 mismatch. Instead of them going to the immigration office to file in person which would be accepted, they just decided to not notify you and not do anything about it. Sounds like it's time for a new agent.

You can do your 90 day report in person up to 7 days after the due date. If that time period has not passed yet, go file at your immigration office.

If that time period has already passed, then you will be fined 2000 baht next time you need a service from immigration.