^ Probably the fact that Red Squadron was involved in the attempted coup in Homefront/Paradise Lost (with one of the cadets even appearing in both that two-parter and Valiant), yet nothing is ever mentioned of that fact in Valiant.
I'll wait for MacLeod's reply to be sure that's what he meant, but for now...
Is that all? Because none of the Valiant's crew wants to talk about them committing treason 2.5 years earlier? Sisko never has an opportunity to confront them about it. Nog shouldn't know about it. Jake shouldn't either.
The way I see it, sending them on patrol aboard the Valiant was done deliberately to get them out of the way and avoid all the questions that would arise due to Leyton's coup.
The timeline for that specifically doesn't add up, but by the end of Paradise Lost, Red Squad has been put into protective hiding with possibly all their identities changed.
SISKO: Where's Cadet Shepherd?
NOG: That's a good question. I couldn't find him anywhere.
ODO: What do you mean you couldn't find him?
NOG: I mean he's gone. And as far as I can tell so is every other member of Red Squad. The rumour is they've all been sent on some kind of training exercise.
LEYTON: I'm afraid Cadet Shepherd won't be returning to Earth anytime soon.
Sisko never sees them again to follow up. The only person whose head we see roll is Leyton voluntarily resigning. A dirty publicized investigation of the event won't do SF much good. By the time Sisko hears of Red Squad again, karma has judged them all guilty and they're dead except for 1. There's at least 1 Admiral, a couple dozen Captains and Commanders, a group of "elite" cadets, possibly some ensigns eventually, and even the Academy Commandant all part of the conspiracy. That's a lot of people with power covering each others' tracks.
I say the timeline doesn't add up (not like I'm checking star dates and doing all that math, someone else is welcome to), because it's nearly 2.5 of our years between the two episodes and...
COLLINS: The training cruise was supposed to last three months. We had seven regular officers and a crew of thirty five cadets. The plan was for the cadets to run the ship while the officers observed and critiqued our performance.
JAKE: So this was a training ship. Like the other one, the, er, the Republic.
COLLINS: Not quite. The Republic's an old ship. I don't think she's left the Terran system in fifty years. The Valiant's a state of the art warship. Our mission was to circumnavigate the entire Federation before returning home.
The war doesn't start until the end of season 5, so the Valiant's mission should have started around the time Garak murders a SF officer at Empok Nor or Eddington dies. Maybe a little sooner.
At the same time, Starfleet Medical and Security along who knows how many Admirals and Captains are covering up Section 31 trying to commit genocide of the Founders and assassinating Romulan politicians. A little treason doesn't sound all that hard to cover up.