The Avengers Were Not Together: After the events of Avengers: Endgame, the team had some problems. Some members retired, went into hiding, or took on different responsibilities. This meant that the Avengers were not a complete group, and they struggled to come together to fight the Skrulls in the Secret Invasion.
Dealing with Other Threats: The Avengers have a big job of protecting Earth from many different threats. It’s possible that during the Secret Invasion, they were dealing with other dangerous situations at the same time. They might have been fighting against other enemies that needed their attention, making it difficult to focus on the Skrull invasion.
Making Smart Choices: Because the Secret Invasion was a big and complicated problem, the Avengers leaders might have decided to focus on specific parts of the battle. They could have chosen to do secret missions, gather information, or fight Skrulls in specific areas instead of getting involved in high-profile battles. This strategy helped them keep their plans secret and avoid exposing themselves to the Skrulls.
Using Specialized Teams: The Avengers are made up of different heroes with different abilities. During the Secret Invasion, they might have thought it was better to use teams that specialized in fighting the Skrulls. These teams, like the Secret Avengers or the Young Avengers, had skills that were specifically suited to dealing with shape-shifting infiltrators. By using these specialized teams, the Avengers increased their chances of success against the Skrull threat.
Trusting Nick Fury: Nick Fury, who led S.H.I.E.L.D., is a skilled leader and strategist. The Avengers might have trusted him to handle the Secret Invasion on his own while they focused on other important tasks. They believed that Fury’s experience and knowledge were enough to handle the crisis without needing the Avengers directly involved.