The implication I read into it was that the Spy has some connection to the empire. She knows enough to warn Celeria about the bugs and she uses something that sounds an awful lot like the Empire's catchphrase when she does it. Given that, it seems likely that she either hacked the turrets or used some kind of known glitch in their programming to get in. The question is whether she's from the empire directly like Alan is, or whether she's a descendant of past survivors of some crash, who are responsible for the Starveek kingdom.
I'm also not sure that the AI doesn't know about her presence. Could be that she simply hasn't told Alan yet, just like how she didn't tell him that in Starveek, co-rulership involves marriage. She's has already taken a ton of personal initiative with stuff like making clone daughters or promoting Alan to commodore and she's already witheld the truth from Alan before, so this sort of thing wouldn't be terribly out of character for her.
There's been too many coincidences here - Starveek having the same name as the empire, ancient "magic" tools that act an awful lot like the technology Alan brought down with him, a "goddess" who sounds like an AI and thus far has only interacted with people who have nanomachines (with normal people having to take it all on faith), and probably more that I don't remember that I feel like this isn't so much a plot hole as something that isn't yet explained directly but will be. It's fairly clear that somebody has been running around in the background doing things in a way that isn't visible to Alan, and this just seems like another expression of that.
That's exactly what I thought too. My hunch is that the Empire already encountered this planet hundreds of years ago (the intro implies their rate of technological advancement is pretty slow). They decided the "magic" native to the world could be helpful in fighting the bugs, and dropped a team to research it and help prep the planet for defense against a bug invasion. Then to prevent the planet from becoming a high-priority target for the bugs, classified everything top secret.
The Starveek name is too much of a coincidence. So it's probably the name adopted by the prep/research team when they founded a noble house to help their operations. The special coin-minting and guild quantum communications tools were probably their doing - provided to all countries to help stabilize the planet's economy and politics. But then they ran afoul of political machinations and assassinations from the natives, and much knowledge of their original mission (known only to the higher-ups) was lost.
The spy is probably a Starveek black operative - one of the few departments which still had daily access and training on the remaining pieces of their Empire tech. She was captured when the Starveek nation was overthrown, and is on death row for being a spy. The story hasn't made clear how she's being coerced to do the bidding of her captors (instead of just running away once she's out on her own). But even if she has some free will, the loss of knowledge about their original mission means she doesn't immediately recognize Alan as an ally. At this point she's probably wondering if he's an escaped Starveek who was pretty high up in the chain of command, or one of the factions which destroyed the Starveeks and got their hand on Starveek (Empire) tech, or (if she's aware of their original mission and extraterrestrial origin) if Alan is from the Empire.
Least that's my guess.
You're missing something about the filters, a computer AI is the one filtering that information out for the human operators. Iris is an AI, the one doing the filtering. On limited processing power of Iris, she is literally recording random conversations in bars around the world. You want to say she can't be bothered to check the shots of weapons that are throwing out lethal force in an area where civilians were recently introduced to and can potentially wander in to the firing arcs of?
If I remember right, Iris only installed listening devices in a few bars that Selena and Sharon visited during their search for Alan. So the processing power needed to constantly monitor those bugs shouldn't be that large. She's not monitoring every conversation in the entire world.
The entire thing is actually based on a real NSA program called ECHELON. They'd wiretap phone calls and listen/record for sigint. Initially this was done by people listening to each call and marking which ones had actionable intel. But if the people who've spoken about the program are to be believed, later versions simply had voice recognition transcribe the calls in real-time, and flag the audio to be saved and reviewed by a human if certain keywords were spoken. Supposedly several terrorist leaders and Osama bin Laden were partially located by slips of the tongue by underlings on cell phone calls. There's a reason these guys use written messages passed by hand, instead of cell phones.
Anyways, the key is that it's not a single-layer filter. Low-level filtering is done at the "boots on the ground" level. With further levels of filtering as the report gets passed up the chain of command. So if the spy hacked the defense turrets to think that she's an ally and to let her pass, then Iris may not be "consciously" aware that the spy slipped in. The data saying the spy was allowed in and the video of her arrival was logged and recorded by the defense emplacement. But no report was generated to be passed up to Iris - because there's no need to bother the higher-ups with reports about "allies" entering or leaving the city.
