Had nearly the same thing happen to me on my way out. Waiting to separate and was told they didn’t have records about AIT and that there was a gap in my records, implying that I wasn’t eligible to separate even though it was at a time when they were drawing down (RIF) and sending guys out the door with less than two years’ service, I had literally rolled from basic into AIT in less than two weeks (same base) so it wasn’t like it was a different base, and I had partly served after AIT at the same base. I told them to contact my ex-battalion commander (now a full colonel and regimental) and ask him why he would allow me to serve without having done AIT, and also why were they sending my paycheck to a base during a time frame that they didn’t have info on me having served at and also how I had been promoted during that time. They let me go with the promise I could get an amended DD214 in the future,
This was the mid-90s and they were ostensibly computerized and networked, but I wondered for years after if I would get a notice that I would somehow be recalled and told to finish my service that they weren’t sure about.