Shift registers - what happens at single clock pulse?
Notice the arrow-head symbol on the clock input of each of the flip-flops. This indicates (rising) edge triggering.



This means that each time the clock signal transitions from low to high, the signal at D gets copied over to Q.

In the ideal case the clock edge is instantaneous, so whichever level is applied at D at that instant, is all that matters. 

Even in practical situations where the clock rise time is finite, triggering is at the transition of the clock past a threshold value. Thus, the read-in from D remains instantaneous.