Yes and no.
Yes, you are absolutely right that no one knows the facts despite this investigation being ongoing for 8 freaking years there have been few leaks.
Yes UConn knew the rules for the APR and the rules did not change. However you are wrong about a key part, the punishment. The punishment was what was changed. During the years UConn was well below the APR level the initial punishment was set at warning, loss of scholarship and then after repeated misses on APR score with no improvement a NCAAT ban. The NCAA changed the punishment without giving schools (UConn) a chance to improve the scores. The scores were literally already in before the punishment was changed. So yes UConn knew they would be punished but the severity was thought to be much lower.
The best way to frame it is knowing the law for stealing a candy bar in a nice area of town is a fine of $100. You steal the candy bar thinking you can get away with it once because you haven't had any issue before, it's not hurting anyone much you don't have any cash on hand and you are hungry. You get caught and have to pay the fine. You are set to pay the fine after some back and forth with paperwork. Suddenly the newly elected judge who you had fired when he was a teenager decides stealing a candy bar is a felony (but only for those who steal from that one store because he doesn't want to be mean to people who live in poorer areas) punishable by a year in jail. Of course this punishment is going to go back retroactively for a year. Even though there are others who have stolen from the store, you are the only one who has stolen in the past year. You knew it was a crime to steal but you didn't know the penalty. Congrats you are fd and in jail for a year.
People are frustrated because of the way this is being portrayed by the media. UConn and Calhoun were demonized for the APR penalty. Cuse is being portrayed as a victim for what may be straight cheating.
Really, many are jumping the gun.