The short answer is, you can’t.

Take this example:
You schedule an employee from 9a-5p.
They get 2 paid 15m breaks and 1 30m unpaid meal.
They clock in at 9a, they clock out at 5p.
They take their 2 15m breaks and their 1 30m minute.

They’ve done exactly what you expected, so the system should approve it (otherwise, why have them scheduled). 

Now, consider if they punch in at 8:59a, is that acceptable? If so, then move the EARLY ENTRY grace to 1m. Is 8:58a ok? Then move it to 2m. And so on until you get to the point that YOU DO want to get alerted. And do the same on LATE ENTRY – is 9:01a ok but 9:02a not? Then set LATE ENTRY to 1m.