The Ancient One not helping to stop Loki's invasion during The Avengers' Battle of New York doesn't make sense. The God of Mischief was exactly the kind of threat she and the sorcerers are supposed to protect Earth from.
In 2012, Nick Fury was finally forced to assemble MCU's founding heroes after Thor's adopted brother made his move to take over Earth. While the team ultimately defeated Loki despite a rocky start, it took them a lot of effort and a near-death experience for Iron Man to do so. As it turns out, while the Avengers were fighting hard to fend off the villain and his Chitauri army, the then-Sorcerer Supreme was casually watching the battle unfold with no intentions of actively helping whatsoever.
When The Avengers was first released, the existence of the Ancient One and Masters of the Mystic Arts was still unknown. The time heist in Avengers: Endgame which saw some heroes revisit the Battle of New York, allowed Marvel Studios to retroactively establish their existence in the MCU before their presence was known via Doctor Strange. The problem with this, however, is it also directly contradicts what's been revealed about the primary responsibility of the sorcerers in the universe.
As explained by Doctor Strange (Benedict Cumberbatch) in Thor: Ragnarok, he's keeping "a watch list of individuals and beings from other realms that may be a threat to this world," and apparently, the God of Mischief was one of them. This was the reason why, when he learned of the trickster's presence on Earth, he quickly trapped him in a void to make sure he was unable to wreak any havoc. The only time he brought Loki out of the alternate dimension was when Thor came in to pick up his brother. Considering this, it doesn't make sense that The Ancient One would opt to lay low, keep the Sanctum Sanctorum safe, but never fully help the Avengers contain the villain when he was on the verge of taking over the planet.
The Masters of the Mystic Arts led by the Ancient One in 2012 were tasked with protecting the Earth from mystical threats and this responsibility remained the same years later but with Doctor Strange now leading the charge. Loki fit the description of the sorcerers' target beings perfectly; aside from his ability to use magic in varying ways, he was also in possession of two Infinity Stones: Mind and Space Stone. Since the Ancient One was the keeper of the Time Stone, she should've known how massively dangerous the villain was at that point in time. Given this, she and her subordinates should've been compelled to actively help in defeating the trickster and his Chitauri army, but instead, she decided to stay put and leave the newly-assembled Avengers to deal with the God of Mischief on their own.
Understandably, Marvel Studios had to find a way to incorporate the Ancient One in The Avengers without breaking established continuity. That said while they may not be able to feature her and other sorcerers more prominently as they did with Doctor Strange and the Masters of the Mystic Arts in Endgame, they could've at least shown her being more invested with Loki's attack as it's clear that she could've done more. That way, it doesn't look like she didn't take her sworn responsibility seriously, only destroyed Chitauris flying over Sanctum Sanctorum.
