these courses aren't designed for convenience, the length is structured to satisfy DTV requirements of embassy officials at the MFA. Minimum safe bet course length is 6 months. Otherwise expect to be given a tourist visa for your 10,000 baht processing fee.
I screenshot everything through the process, including the final completed applicant details page, I have a complete record of my submission details. I suspect you were sloppy and didn't triple check everything.
In the big picture you're going to have to do a border run regardless after your extension, so you might as well get used to it now. It's a lot less headaches than multiple trips to immigration.
I don't know what planet you get your news from but Thailand is starving for tourism the last thing they're going to do is choke out this scheme in the near future.