In the level where you have to go to the church, when you enter the church you see this invisible alien, when you chase him, a cutscene comes up and after the cutscene you're 10 stories high.. I've also had this sequence when the aliens invade and you fall out of the chopper (when lockheart captures you), I had to kill some aliens and after killing all the aliens you see this alien pod falling from the sky, the objective is to escape but while running to the objective, the mission ends. The next mission started with Alcatraz laying on his back.. I thought it was weird and decided to youtube a walktrough up to that point, and the player who made the walktrough had a different experience. In the walktrough, when you try to escape you encouter a bigger alien who shoots you down, explaining why I woke up on my back the next mission