— 𝐇𝐎𝐖 𝐃𝐈𝐃 𝐒𝐓𝐀𝐍'𝐒 𝐁𝐎𝐃𝐘 𝐄𝐍𝐃 𝐔𝐏 𝐈𝐍 𝐓𝐇𝐄 𝐌𝐀𝐙𝐄?
The Creators (WCKD) took it there during the night. If you think about it, you'll realize they must have a lot of scientific knowledge and machines. Moving a body isn't hard for them.

— 𝐖𝐇𝐀𝐓 𝐇𝐀𝐏𝐏𝐄𝐍𝐄𝐃 𝐓𝐎 𝐓𝐇𝐄 𝐍𝐎𝐓𝐄𝐁𝐎𝐎𝐊?
It was still in Minho's pocket when he died. Thomas took it out. Had a peek at it. That's also why he knows about the "There is nowhere you could go that I won't be with you", as it was underlined.

— 𝐇𝐎𝐖 𝐃𝐈𝐃 𝐌𝐈𝐍𝐇𝐎 𝐔𝐍𝐀𝐋𝐈𝐕𝐄 𝐇𝐈𝐌𝐒𝐄𝐋𝐅?
Honestly, just imagine what you want.

— 𝐇𝐎𝐖 𝐃𝐈𝐃 𝐓𝐇𝐄𝐘 𝐍𝐎𝐓 𝐍𝐎𝐓𝐈𝐂𝐄 𝐙𝐄𝐄 𝐅𝐀𝐋𝐋𝐈𝐍𝐆 𝐃𝐎𝐖𝐍 𝐓𝐇𝐄 𝐁𝐀𝐋𝐂𝐎𝐍𝐘?
Plenty reasons. First of all, glass shattered everywhere when the Crank jumped out of the store. Half of the Gladers covered their eyes. After that, they were too focused on saving Newt. And the way the Crank and Newt bumped into Zee so suddenly shocked her, too. She didn't have time to scream before she hit the ground. And a hit like that, straight on her back, knocked the wind out of her, so it was impossible to yell for help. By the time she could, the Cranks had already devoured her, and the Gladers were already gone.