I can't blame her. I don't think she even had a scene with Tom Holland. She came out for her cameo after Peter left, and she was just with Tony and Happy in a scene that advanced Tony & Pepper's relationship in a big way, and that did really feel like a scene from an Iron Man movie that briefly intruded into our Spider-Man movie. So from her perspective, it must have seemed like it was for an Iron Man movie.
She says in the clip she thought it was Avengers, which makes sense since since Infinity War was right around the corner.