Discount Geek’s review published on Letterboxd:
How does MJ know that Mysterio know that both she and Ned knows Peter Parker is Spider-Man? She said this directly after Mr. Dell’s Voltron reference. Peter did warn that both of them are in danger for knowing who he is but that was before he accidentally told Mysterio about MJ and Ned knowing. She clearly states that she knows Mysterio knew she and Ned knew Peter’s secret so she and Ned can try to escape but nobody even concretely confirmed that to her beforehand.
This is something that I even noticed the first time watching the movie in theaters.