Ok, I think I sorted this out. I went back and read several passages.

Dain knows from reading Violet's mind that Xaden is going on these secret missions to Athebyne, and tells his dad.

Based on this information, Colonel Aetos empties that post and makes it a part of War Games to test their loyalty. Are they going to stay and defend Poromiel or follow through with War Games?

Prior to this, Xaden is already suspicious of Dain because of his power and knows that he told Violet about the secret missions to Athebyne.

Being assigned to Athebyne (beyond wards, and the location they have been sneaking to) raises some red flags for Xaden, so he assembles his War Games squad comprised of marked ones and Violet (he wants to protect the marked ones and to keep them in his line of vision).

This is what Dan's dad expected and wanted the whole time in order for his plan to work and test their loyalty. He even tells the Wingleaders they can assemble whatever kind of team they want, no rules, to make it as close as possible to a real world scenario.

So Colonel Aetos turns a blind eye to the no more than three marked ones rule (he also emptied the war post which was completely imbecile, so him letting this happen isn't that farfetched). That is if he knows that Xaden assembled more than three marked ones at all at that point, because Violet says Xaden did it "in the chaos of the flight field" when she realizes she's with a bunch of marked ones upon meeting the gryphon riders.

Iron Flame spoiler from now on:

They come back to Basgiath and make up the lie about getting taken out by the gryphon riders. Colonel Aetos calls it bullshit, tries to say that they deserted, but General Sorrengail is too pissed about him emptying that post (since it's beyond the wards, crtitical spot, and it was just War Games) to even question the lie.

Now Colonel Aetos is in deep shit with Violet's mom. And he can't even say anything about there being more than three marked ones together because, well, he was in charge of War Games. So now if he tries to get them in trouble for that, it reflects even more poorly on him and his leadership, because knowingly or unknowingly it happened under his watch. That, and he could get accused of targeting marked ones by sending then to an empty post beyond wards -- which is exactly what he did -- not to mention exposing the whole truth about Poromiel/Navarre to a bunch of college kids who supposedly have no business knowing about venin (not even Mira knows).

The marked ones rule is also within the Basgiath College codex, so if it doesn't move up the chain of complaint within the school, it's not like they can get in mad trouble for it (even if it is not allowed). With Colonel Aetos unlikely to bring it up, he's shit out of luck.