If there is a standard operating procedure governing this kind of situation, and she violated it, then I withdraw my argument.
I think maybe that's the real issue here, though. I don't know if Bioware had any military consultants reviewing the ME series for them or if any of their people have been in the military, but my guess is that military accuracy just wasn't at the top of the agenda for the writing staff. (And I'll admit that I know precisely jack about this and military inaccuracies probably just fly over my head.) To the extent that Shepard, Ashley, or anyone else sometimes betrays lack of military discipline or proper procedure, it's likely an unintentional side effect rather than something that actually defines their character, *unless* it is called out as such in-game. While Shepard can reprimand Ashley for approaching the beacon, Anderson doesn't seem to think it's a "you don't belong on the Normandy"-level offense, and if Shepard agrees with bringing Ashley on board, Anderson comments that Kaidan agrees too. So it's evidently considered a relatively minor breach in terms of how we're meant to view her character.
It's kind of like the people who like to argue that the Empire aren't really the bad guys in Star Wars or that the Rebels are unworthy of taking their place because the Jedi are elitists, because innocent people are killed when the Death Star blows up, or whatever. The politics aren't the point of Star Wars, and Lucas apparently means for the Rebellion and the Empire to stand as archetypes of good and evil, so that argument really just boils down to an argument that the story itself is flawed. If innocent people are killed when the Death Star blows up, that doesn't tell us that Luke Skywalker knows that and doesn't care. It tells us that he isn't written well enough to consider it or have an opinion about it in the first place.
Basically, yes it isn't quite written well enough to consider it. I see your point, and for the sake of not running this whole argument ad nauseam, I'll say that this is the best argument against my statement here: simply put, the story isn't complicated enough, and understandably -if regrettably - so.
Personally, I want to see something based on speculative future fiction of our own Earth to take things seriously and keep it realistic, implementing modern logic and tactical thought (and translating it into future principles that would apply). I think a strong basis in reality in practical narrative was required here. Since it is a futuristic ideal of the current timeline, Mass Effect's lore needs to be heavily based from modern reality. From there, they can take the liberties they require, provided they are explained and elaborated on, since it is meant to be a relatively hard, if slightly fantastical universe. Said lore then must be the basis for the story, and the story must not break that lore or narrative possibility. Any breaks in the lore must be properly and adequately explained. From those constraints, they can make their story.
That's my personal opinion.
Therefore, if there is a standard operating procedure based on modern logic as I stipulated, I'd like to see it translate into Mass Effect. I'd like a speculative fictional future of Earth to be as technically accurate as possible. And I'll tell you, said logic is not like the hopeless ideal of perfecting the art of fighting the previous war in time for the next, but to maintain a capability to perform and adapt to situations as necessary. These are basic situations that are going to need to be fulfilled no matter what war you fight. You have an enemy that lays a bomb-trap? Secure the area and send in Engineers or EOD for proper disposal. Secure an enemy encryption device? Secure the area, get the SIGINT group from the S-2 shop in to send it up the CoC. Capture an EPW (Enemy Prisoner of War)? Secure him, call the MP's, take him in, then call me, the HUMINT guy and my team in for interrogation or interview.