With the release of Boruto: Two Blue Vortex chapter 4, fans were introduced to the new antagonists of the series - the Divine Trees. From the chapter, it seemed very evident that even a single Divine Tree was very strong, let alone four of them. This was why Boruto was forced to run back to his hideout.
That being said, Boruto did not even unveil his complete power to fight the Divine Tree in the first place. While there has been a time skip of three years, as evident from the flash forward from the series' first chapter, the protagonist can use the karma seal. Then why didn't he use it to fight the four Divine Trees, let alone rescue Sasuke?
Disclaimer: This article contains spoilers from the Boruto: Two Blue Vortex manga.
Why didn't Boruto use karma to fight Divine Trees?
From the very beginning of the new manga series, it has been Boruto's goal to rescue his master Sasuke Uchiha. He was so fixated on his goal that, despite the toad's warnings, the protagonist kept fighting the Divine Trees until he got trapped by one of them. If he was really so desperate to rescue Sasuke, why didn't he just use his karma seal?
While the manga hasn't confirmed why the Otsutsuki refrained from using the karma seal, there could be several reasons. However, most of them track back to the manga creator Masashi Kishimoto, and not the series' protagonist.
From the flash forward where Boruto could be seen using the karma seal, it is very evident that he could use Momoshiki's powers. Hence, the reason why Kishimoto may have refrained from using it may have been to show fans just how strong the protagonist had become during the time skip. Despite Code being known to be stronger than Jigen, the protagonist could defeat him without using the karma seal.
Moreover, in the flash forward, when Boruto activated his karma seal, he also activated his jougan. Thus, there is reason to believe that after the Otsutsuki lost his right eye, activating the karma seal resonated with his dojutsu, forced the activation of his jougan. If the jougan were to be revealed this early in the new manga, it might tarnish the story's pacing due to the lack of build-up for the same.
Another reason could be the protagonist's resolve to not use Momoshiki's Otsutsuki powers and stick to his Shinobi routes. If Boruto were to use his karma seal, he should be able to access Momoshiki's experiences and abilities. This should have effectively allowed the protagonist to use the Otsutsuki Space-Time Jutsu for traveling. Instead, he stuck to his Shinobi routes and learned the Flying Thunder God Technique.
Meanwhile, Kawaki completely relied on karma for his powers. This meant that he was almost powerless against the protagonist in his base form.
Lastly, the reason for Boruto not using his karma seal could be tied down to Momoshiki himself. The last time the protagonist extensively used the karma seal, Momoshiki was able to take control over him. Therefore, he may have deduced that using the seal effectively made him susceptible to Momoshiki's control. Hence, he may have refrained himself from using the powers to avoid such scenarios.
The only other scenario could be that Momoshiki did not want to let his vessel use his powers anymore. When his prophecy about the protagonist losing everything became true, he expected to gain control over his vessel's body. However, his vessel seemingly did not lose any hope, which irritated Momoshiki. Thus, he may have decided to not let his vessel access his powers to make his life tougher.
That being said, these are just theories. Thus, fans may have to wait until future chapters of the manga to confirm why the protagonist did not use his karma to save Sasuke.