When Freddy discovers Jason's weakness to water, he adds insult to injury by showing the dismembered head of Jason's Mother in front of his child form. Now Jason is a Genius Bruiser when it comes to killing, everything else however he is not so smart. So when he sees his mother's head he comes to the logical conclusion (in his point of view.) that Freddy killed Mrs. Voorhees. When Freddy enters the real world, Jason even stops going after the others just to confront Freddy.