While Captain Marvel answers a lot of questions - like the issue of Nick Fury's eye, how the Avengers got their names and why Ronan is so obsessed with Infinity Stones - it also left a few choice ones hanging in the air. For a start, while Nick Fury was told that using the pager was only strictly for emergencies, that's not enough to explain why he didn't class a world invasion and the potential destruction of the planet as emergencies. And then there's the issue of the missing Skrull.
When Talos' Skrulls come to Earth and immediately embed themselves, there are four survivors. One becomes the old lady on the bus, one becomes the SHIELD director and one becomes Agent Coulson temporarily. The fourth's hidden identity is unclear, so the old lady is either Talos' science officer or the mysterious fourth character.
By the end of the movie, Talos has escaped, the Coulson Skrull is dead thanks to the car crash with Nick Fury and the science officer has been killed by Yon-Rogg. So where's the fourth? Is the old lady still out there somewhere?
It can't just be a plot-hole. Talos' whole drive is to preserve the safety of his people - whether that's by violent acts against the Kree to defend themselves or by making sure they are safely embedded on other worlds. As his reaction to the death of the Coulson impostor proved, every one of his people is precious to him. The idea that he would simply abandon one of his own without a second thought is inconceivable. There has to have been a reason.
Captain Marvel's big twist on the Secret Invasion story has made most fans who know the comics suspect that we won't be getting to see that storyline at all in Marvel's "Phase 4". Sure, we might get to see Skrulls again in Captain Marvel 2, because there are loose ends like Ronan, the search for the other Skrulls, the destruction of the Kree by the Nova Corps and the reason Captain Marvel really stays away, but the idea of Skrulls as nefarious impostors on Earth now makes no sense.
But something of that storyline could persist. That missing Skrull could have been left by Talos consciously on Earth...