Well, Cloud was supposed to find something amiss, I guess. Jenova was manipulating him.
But the fact remains that if Cloud had the ability to open the cell door, he'd have done it before they all fell asleep. There's many more flaws, which leads to more assumptions, to believe that Cloud released Jenova.
I don't think Jenova opened the cell, either. As I said, I believe it was the soldier, running from Jenova. He died just as he was opening the door, and didn't get the chance to go through.
