I've had this weird/annoying problem appear a few times now in Mathematica 10.4 where whenever I click, it highlights everything from the bottom of the cell to my cursor. If I click outside a cell, it highlights all cells from the bottom of the notebook. The problem goes away temporarily when I quit and restart, but I can't figure out how to fix it otherwise.
Edit: If it helps, I've figured out that it seems to happen when I bring another application to the foreground and then switch back to the Mathematica window.