Alternately, it initially seems like Alice is some kind of under-promoted superhero, but she didn't actually do what we thought she did, and there's nothing really special about her.
It turns out that Alice is actually the leader of whatever organization she's in. She just likes to disguise herself as a janitor for whatever reason.
...but even with the promotion, she's way overqualified.
Alternatively, Alice didn't directly do what we though she did, but did the job of a commanding officer in organizing those who did, displaying an uncanny talent that's going to waste.
...but it turns out that she really is just a janitor, she just likes to pretend she's in charge to make herself feel better.
Alice is basically a God-Mode Sue capable of resolving all the in-story conflicts in less than 30 minutes if she ever felt like it; however, she's so happy in her job as an errant musician that she couldn't care less about the world's problems.
Alice's power decreases the higher up she gets promoted.
Alice is a Jerk Ass and/or Deadpan Snarker who would rather stand around and clean the floor while pointing and laughing at the heroes busting their asses trying to save the world than actually helping them.
Alice is a very competent specialist that just opted to be a janitor because she doesn't like responsibilities. But occasionally she shows her assets, only to be rejected because of her low status. And she still saves the day behind everyone's backs, using the limited resources of a janitor.
Alice is a has exceptional leadership and tactical abilities that she occasionally uses in the field. She routinely displays abilities suited to high-ranking commanding officers when allowed, but can't be promoted farther, as she's not trained as an officer. While offered many incentives to be promoted, she prefers not to undergo the additional training, as she wishes to continue to be in the field. Higher-ranked officers routinely make bets on whether the new incentives and arguments will get her to change her mind, and often allow her 'suggestions' to become their orders.
Alice is extremely skilled and highly qualified for a leadership position, but she's only employed as a janitor at a big powerful business. THEN she reveals that she's actually the mastermind of the whole whole operation, and only acts as a janitor to maintain confidentiality. BUT in the end we find out that not only is she NOT the mastermind of the operation, it turns out she isn't even a janitor.
Averted: Alice is routinely promoted at regular intervals.
Enforced: "Hey, those losers in the audience need a character that's better than their job to sympathize with!"
Lampshaded: "Why hasn't Alice been promoted yet? She killed Emperor Evulz and she is still a fry cook!? It doesn't make sense!"
Alice is an extreme case of Brilliant, but Lazy, and a promotion to a higher rank would imply a lot more work and responsibilities for her, so she downplays her skills to fool her superiors and stay on a lower-profile, but more relaxed job.
Alice is kept in a seemingly low position so that the organization's enemies don't notice her. After all, who sends assassins after the janitor?
Exploited: Alice is The Mole, and while being competent is benifical in her work, she keeps a low rank to avoid unwanted attention to her actual work.
Defied: Alice actively tries to get promoted.
Discussed: "We can't pick Alice for our team to go fight Emperor Evulz! She's just the janitor." "But the low-ranking ones are always the strongest! She's our secret weapon!" "Come on, the only creatures she fights are dust bunnies. This isn't a movie."
Conversed: "This isn't fair! Alice was the one that saved everyone's arse back there, and instead of being her the one recieving the new rank, the superiors promote that vain and conceited fool Trevor?! What the hell!?"
Alice's superiors are perfectly aware of her great talents, and that's precisely the reason they actively keep her in a low position: If they gave her the opportunity to grow, she would eventually turn into a menace to their power and ambition. And to make themselves sure that she doesn't abandon the organization to look for a better position, they use nasty extortion tactics to keep her binded. This lack of recognition and constant pressure eventually turns her into a mentally unstable individual.
Alternatively, Alice's knowledge that she far outstrips her peers gives her a massive superiority complex. However, this heavy pride is the one thing that keeps her stuck on her low position. The superiors cannot trust someone that's not a team player with a greater rank.