Pressing the button on the device in the attached screen shot causes the piston to pump for one and a half seconds. Afterwards, the diamond block is on top of the sand block.

The glitch only occurs if the system is run for an odd number of redstone ticks, so it doesn’t happen if a stone button is used.

The comparator contraption is a 2-clock. If it’s replaced with a 3-clock, the glitch does not occur. Since the goal here was to build a high-precision binary timer, that’s not a very attractive workaround. (No, really. It only looks like a sand duplicator component. )