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I'm not exactly sure of all of the legal stuff but according to some of the comments on the video Fox owns the rights to use the skrulls in movies due to the fact that they own the rights for the Fantastic Four still. I'm not sure if this is true like I said I just took a quick look at the comments
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from what i read, fox only owns the rights to the Super Skrulls, while Marvel owns the rights for the regular skrulls