Sorry to hear about this! I had a similar experience, except with a community college credits from a dual credits course I took in high school. The application undelivered and bounced back to me after two of my deadlines (1/1) had already passed, so I essentially missed those deadlines (and I had already paid for those schools apps too). Luckily, I was able to get my missing transcript in and submit my applications to my Jan 15th deadline schools, but I was very close (as in I submitted on the 15th).
So, basically, if any of your transcripts indicates previous course work from another institution, you need to send those transcripts from that previous institution. Otherwise it will be undelivered.