That's been my thought, since we only saw a fairly small group in Capt. Marvel.
I haven't read it yet, but from what I've read about it online the invasion in the comics is lead by the Skrulls' queen, Veranke, so perhaps it could be that Talos' faction broke off from the rest of the Skrulls before they arrived on Earth, and now Veranke's more hostile faction has arrived.
Or it could be the other way around. CM portrayed the Skrulls as a people oppressed by the Kree. Some victims of oppression just want to get away and live in peace, but oppression also generates resistance, which often escalates to the point of extremism or fanaticism. The Secret Invasion could be the work of a extremist splinter faction within the Skrulls, with Talos representing the mainstream.