What it looks like to me: in business they talk a lot about "having your ducks in a row". It seems to me that your colleague had his ducks in a row but his professor scattered them, so the university is taking responsibility for the professor's bad behavior kind of, but they are still making the colleague arrange the ducks in a row again, which still kinda stinks.

As for you, your ducks ran wild kinda from the beginning. They never saw you get them in a row the first time, so it is reasonable in their minds that they dont know if you can line them up or not, compared to the other guy who already did it once. They are not judging your whys or wherefores here. Do you see the difference this way?