I think ML's manipulating Anise (our MC).
1. He knew Anise was powerful from the start. It's not clear if he knew that Anise had saintess powers or at least saintess-worthy powers in the beginning, but he knew he wanted her on his side. This wouldn't normally be a problem, since he's one of Farglow's generals, and that means that he's skilled at recognizing power, if not for point 2.
2. He attempted to use his charm powers to get Anise on his side. He didn't know Anise wasn't susceptible to charm in the beginning, so it's clear he did it with malicious intentions. Of course, we don't know whether he would have released his charm power on her immediately after, but this isn't likely. Why would he release his charm on her if it worked?
This was brushed off in the manga, but what if Anise had been susceptible to charm?
This also makes the priest highly suspicious too, but I'll get to that later.
3. He withheld information from Anise, and he does this constantly. Of course, for a general, this is to be expected. But he didn't tell Anise his plan to reveal her as saintess, which means that Anise had no choice but to cooperate with him when the moment came.
4. Before he attempted to use charm on her, he already knew that she wanted to be a refugee of another country. The ML is also good at reading people, and someone like Anise, who wears her intentions on her sleeve and can't lie or evade questions, doesn't stand a chance.
That means that he probably already knew that Anise didn't care for Origlow in the first place, and that his speech about Farglow "being on defense from Origlow" and "we promise to treat Origlow, your home country, right" and "we just want the war to end" was purely made to gain sympathy from her.
Not to mention that Anise didn't know that he was the general. This either means
a. She doesn't have much knowledge of the world, and ML knows this from her inability to recognize him. This supports my point. This also means that everyone is incompetent, from the guards to the prince. This doesn't support why the fake saintess was able to recognize him though.
b. The general isn't very recognizable. This supports my "priest is suspicious" theory.
c. The ML can control when and who can recognize him as part of his charm powers. This explains why only the fake saintess was able to recognize him (he allowed her to recognize him to gain sympathy from Anise). This also supports my "priest is suspicious" theory.
There is probably more, and I'll probably have a field day with finding evidence for it, but I'll leave it at that for now. Now for the priest.
1. He's an ex-soldier, and the manga doesn't specify which country he served. He probably served Farglow, judging by his ability to recognize the general. And despite being able to recognize the general, he never told Anise anything until after ML revealed it himself.
2. The ML trusted the priest enough to use charm on Anise around him. The ML could recognize skill at a glance, and that means he knew the priest was powerful, powerful enough to recognize charm when he saw it. Yet he still tried to charm Anise. This also supports point 1, where I theorized that he used to serve Farglow.
3. He allowed ML to charm Anise, only commenting on it after it failed.
4. He was able to recognize the ML as Farglow's general at a glance, despite the other characters (except fake saintess) not being able to.
Of course, it's fake saintess's fault for antagonizing Anise in the first place. From her initial attempts to kill her to her attempts to kill her now, Farglow doesn't even have to try to get her on their side. They don't even have to make opportunities to gain Anise's favor. Origlow does that for them on their own.
Unfortunately, I don't think their suspicious behavior will ever be touched upon in this manga. It seems completely self-indulgent, just Anise being powerful and destroying assholes and the country who treated her wrong. I sincerely hope I'm proven wrong.