It appears that there really are conflicting stories here afterall. The school sounds like they are essentially backtracking on what was initially put out from the beginning.
Petula Dvorak: No misrepresentation of treatment of piano prodigy by D.C. schools - The Washington Post
So it sounds like this, given the info we have from the school. Before the girl went to Munich, the parents talked to the school, explaining what was going on. Instead of excusing her then, they said they couldn't excuse her absences (or at least someone at the school, likely this "attendance specialist") despite the fact that this girl had what most schools would consider a brag-worthy opportunity due to her talent, and had a plan set up to deal with her academics. Sometime later, after she got back from Munich and after the first truancy letter/phone call (at least) was received, and emails were exchanged, the parents were told, don't worry about it but never informed that the absences were actually excused. They still received at least one more letter about the issue, warning about consequences of truancy, after they had already withdrawn their daughter from the school since that was done after they had gotten home. The journalist claims to have seen the emails.
In D.C., a 13-year-old piano prodigy is treated as a truant instead of a star student - The Washington Post
Essentially, it sounds like it took the school about 5 months to actually change the absences from unexcused to excused, after she had already been withdrawn from the school by her parents.
Statement from DCPS Chancellor Kaya Henderson on Post column - The Washington Post
So it sounds like the problem is that they were having communications and/or redtape issues, rather than computer error/system issues.
And really? After 5 months, the school thinks that there wouldn't be some issue with their child's very excusable absences marked as unexcusable wouldn't be the reason she would be removed from their school? Even after just a month or so, with the "attendance specialist" telling them that she couldn't excuse her for a trip to Munich I could see as an issue.