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Setup time is a flip-flop specification that is typically provided to you by a manufacturer, and is relative to a single clock edge into a flop.
However, setup-violation occurs when one driving flop feeds a signal into a second receiving flop, and the propagation of the signal between them takes too long (due to logic and routing delays).
There is an entire clock-period for this signal to propagate to the receiving flop, minus the setup-spec and the output-delay.
This is a fundamental digital synchronous timing concept - what is your level of familiarity with this?
Take a look at this: **broken link removed**
And, refer to parts of the diagram on page 5 so you can be more specific if you still have a question.
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