Two incidents that I can remember. One was from when I was in JH or HS (can't remember exactly when) was when Lincoln Pius X was forced to forfeit a few boys basketball games because a player had played in a YMCA league at the same time. Nebraska forbids outside participation during the season. Pius went from being the number one seed for their district at 18-0 to the 2nd seed at 13-5 or something like that. A huge hit on them. They eventually got to state with a record of 16-5 or something similar to that. If they had remained undefeated, they probably would have breezed into the championship game, but because of their record, they had to go in as a middle seed and got knocked out in the first round by a team who was on a late season roll. The main thing was they caught it just before the districts started, so it didn't foul up their advancement in postseason, just their seeding.

Second one was in Omaha recently, when Westside's football team was forced to forfeit all but one game. They discovered they had a potential ineligible player just a day or two before they were set to play in the state quarterfinals, so they benched him to be safe. They won the game to advance to the semifinals, and kept him benched while checking out his eligibility. Got eliminated in the semifinals at 10-2, and a few days later, it was determined he was in fact ineligible for 9 of those games, so those games went down as a forfeit, and Westside's official record ended up being 1-11 as a result.

In the first case, the only reason it was discovered was that a kid from a rival school went to watch a friend play, and noticed the Pius player and said something to his coach the next day, who reported to administration and the ball got rolling. (I remember it vividly because I knew some of the kids from the rival school, and they threw the discoverer a party as a reward!)

In the second case, I have no idea how the ineligibility was discovered, but I think it was very similar to the case in the OP, that it wasn't discovered until something popped up in the computer system.