Voltage in an RC Circuit
It doesn't make sense to anyone, I suspect, unless you have a measurement error.


Check that your scope is on DC setting.
Check that if you are using 10:1 probes that the trim capacitor adjustment is correct.
Put both probes on the squarewave and confirm that they are identical.


In the end you are expecting about 4.965 V and seeing 5.002 V. That's an error of 0.7%. How does that compare with the scope specification?