Nick Fury fought Hydra spies long before the Skrull Resistance established themselves, and the Skrulls could've adopted Hydra's more secretive tactics. Before the Secret Invasion series, Captain America: The Winter Soldier was the first Marvel Cinematic Universe attempt at a spy thriller narrative with a superhero twist and featured Hydra as the main villain. The threat of clandestine infiltrators is not new to Nick Fury when Secret Invasion continues his story.
Source：https://www.cbr.com/captain-america-winter-soldier-hydra-better-secret-invasion/
