You may or may not get any grief about previous 90 day reports.. But any action is likely not to be drastic.. The Imm Officers in Bkk can handle the fiasco of your Application be handled in Chonburi as you had no control over that.
I know of a case similar to yours where the fellow's 'Visa' filing was in an office where he did not reside... Turns out the reason for that was the Visa Agent knew an Immigration Officer in that other city that could be bribed
You should post photos of the Visa pages with ID info marked out.. the members will show you what it really says.. And the issue of what you have in stamps in your passport has an important bearing on how your missed 90 day reports will be treated.