They might stick you with a 2k baht fine for being late, but it won't affect your visa. Go to your nearest immigration office and explain. Bring some cash in case you don't get an understanding officer.
First report in person. Then, if you can get it to work online, do it that way. I have yet to successfully submit through the online portal though and have no idea why. However, going in person usually takes about 5 minutes tops, so it's nbd.
Monday was a holiday and today is Thursday. Chill. Songkran is this weekend, so if you don't get it by tomorrow, you'll prob be waiting a while longer.
sometimes the security check on the card can cause an issue. But some shops allow cash on delivery. Or, in the meantime, see if a friend can help you and give the payment to them.
Also, if you haven't already, check with your card to make sure they didn't reject the attempt to connect it to the app. They might have auto flagged it as fraud or something.