I can only suggest you have obviously/maybe entered incorrect information? I have just done my 90 day online after being out of the country (did have a re-entry on my visa) and changing address since my return , being assured and have photos that my new TM 30 has been done. My previous online applications were accepted so this could be interesting! My agent only charges 100 baht for 90 day reporting so if I have a problem I'll be straight down their office.
Had an absolute nightmare when I downloaded the app and everything seems backward eg how much baht you want? not how much currency do you want to send, wiped the app as soon as poss.