Even without the suspicious looks from Misa and the princess herself, I would have been suspicious of Princess Serenity.
Something about her just seems . . . off. She seems quite up front: Polite to the crew once she understands the situation, puts on a nice face for everyone at school, and she tells the crew of the Bettenmaru straight up that she would like their aid in seeking out a ghost ship (the same ghost ship that Marika and Chiaki saw earlier in the series?). Doubtless she has some personal connection to this ghost ship. However, I can’t help but think there’s something more to it than even that, though I cannot put my finger on what exactly that is.