Stupidity: The prison where Magneto is held should have had a contingency plan just in case of escape, like machine guns outside the cell, or tranquilizer darts, or gas.
Suggested correction: What good would machine guns and tranquilizer darts be against a man who can literally control and manipulate metal? As for gas, the area outside the cell is so large that any gas would quickly dissipate before it could be effective.
Stupidity: All the mutants on the island need Magneto at the last second to take control of the missiles so they don't land and explode. Why didn't Azazel just teleport everyone off the island?
Suggested correction: Given the situation, there was probably very little time to come up with a plan like this. The missiles were flying towards them extremely quickly, and there would have been nowhere near enough time to band every single person together for Azazel to teleport them all out of there in just a few seconds.
There was plenty of time. He could have taken 5 at a time down the Beach 3 miles and came back for the rest. Earlier in the movie he was moving so fast men were falling from the sky at nearly the same time and he was teleporting them one at a time.
Stupidity: The X-Men depart for space on a vehicle not designed for space, for an incredibly dangerous mission they know nothing about (and none of them can survive in space at that point), but don't suit up for it in the slightest - and with Nightcrawler and Quicksilver's powers as they are shown later, it'd be easy to do it without wasting time. Not only that, but Xavier communicates with NASA to get the briefing only after the X-Men have already departed.