Canon right now splits the pixel in half and uses the difference in the signal from the one half and the other half to determine how far away the focus is. Using this information Canon can calculate the distance the lens has to move to focus on the target at that pixel. However, this method is prone to be very inaccurate if the lines of contrast that you are focusing on, are aligned to the split of the pixels, since then the signal difference would be minimal. This means that usually these sensors are better suited to focus on vertical lines, versus horizontal which they can struggle with.
