I think I have encountered a small bug in the control-moving mechanism of atom. The mechanism I am referring to is when you hold the left control key whilst having selected some text, and then use the arrow keys to move the selected lines.
The bug only occurs when the newline character is the last selected character. It shows up as a white selection bar. Here is an image.
Having this selected, moving up works, but moving down does not. The pointer will always stay two lines in front of the last line. The newline is selected by moving to the last iterable character, holding shift, and pressing the right arrow key.