Sometimes a 555 timer does not output a great square wave from 0-5 V. In this case, when using it as a clock source for a flip-flop, a bad 555 timer output can lead to missed clock pulses and seemingly strange behavior on the output. To correct this, use one or two Schmitt inverters (7414) at the output of pin 3 on the 555 timer to clean up the output. A Schmitt input has the property of turning a signal that may not have a sharp transition into a signal that has sharp rising and falling edges. A schematic of this is below.
