The exact same thing happened to me. I called their office probably around 10 times over a month and a half trying to fix it and get rid of the red exclamation mark, but they said it was just a "glitch" in their system and that my application was complete and under review. Two months and three days after my I submitted my completed application, they marked my application as complete with a green check mark on 10/10/2014.
Everyone at the front office has insisted that we are fine. However, after talking to some other students, too, I have a feeling that this isn't the case. The same exact thing happened to my friend last year, and he never got an interview at TTU Lubbock despite having a 3.9 and a 35 and being a TTU undergrad -- a school which has historically given a very large preference to their undergrads. This year, he did indeed get an interview at TTU Lubbock and he swears that it was their weird electronic glitch in their system that prevented the evaluation of his application. In fact, last year during the last cycle, Texas Tech emailed him in May saying they never got a completed application from him, despite the fact that he had completed everything and had received interviews at multiple other schools in the state. He had that exact same red exclamation mark on his seconday app.
It's just my hunch, but unfortunately for us, I think that this glitch delayed the evaluation of our applications by 1 or 2 months, depending on when you originally submitted. Despite what the front office told me, I think the red exclamation mark on our app electronically flagged our applications. I have discussed this issue with other TTUHSC faculty and physicians and they think this is the case, too, unfortunately, and ultimately I believe that it their collective concern that led to a resolve of this issue - albeit a very late resolve.
Just out of curiosity, but when did you two take your MCATs? Everyone I know that this has happened to, including me, took a little bit later MCAT. I took mine in June. I think the glitch (that I think they have now fixed) had to do with submitting an MCAT score onto your app after you had already submitted the primary TMDSAS application. For whatever reason, I think that TTU didn't realize you had a valid MCAT score on your app unless it was already loaded onto your primary app upon submission.
Anyways, I really hope that this funky little glitch doesn't cost us our chances here, but I think there there is at least a chance that it did, unfortunately. Sigh. Glad to know I'm not alone, but I'm sorry to hear that this happened to yall, too. Such a silly and potentially unfair thing to have happened during an already stressful time.