It’s tempting to look at a long-running serialized franchise like the MCU and assume that there’s always a plan, but the simple truth is they aren’t always playing three-dimensional chess. Sometimes stories change course over time. (Remember in “The Incredible Hulk,” when Tony Stark invited General Ross to be an Avenger? This was ultimately forgotten and retconned.)
It’s possible that Everett Ross was a Skrull the whole time but that wasn’t always the plan, so it just doesn’t perfectly sync up to the canon. Or maybe he was supposed to be replaced relatively recently and they made the reveal a little confusing.
Example: In the first episode of “Secret Invasion,” we learn that when Skrulls replace a real person, they prefer to abduct that person and use advanced technology to (apparently) download their memories. So you’d think that, if the writers wanted to be clear about this, they’d have shown Ross inside that Skrull compound, hooked up to one of their machines. But they didn’t, either because Ross was always a Skrull, or because they only had Martin Freeman for a couple of days of filming and didn’t think to get any shots of him inside a sci-fi stasis unit.
The fact that the episode continues apace and every single one of the main characters drops the subject, instead of talking about how they need to find out if Ross was always a Skrull, or if they need to rescue him, suggests that “Secret Invasion” doesn’t want us to wonder either, which in turns hints at a very unsatisfying answer. As always with serialized stories, we just have to wait and see. Hopefully, they get around to this eventually, because we want to know. And I’m sure Ross’s ex-wife Valentina Allegra de Fontaine (Julia Louis-Dreyfus) — the CIA director in the MCU, as of “Wakanda Forever” — probably does too.