Can I dispute a penalty if I filed on April 15th and paid using a credit card because they did not extract the money from the credit card until April 16th?

[Opus 17]

You can ask, but since the tax system is pay-as-you-go, it's possible that the penalty is not only for the tax you owed on the filing deadline, but for estimated payments you should have been making throughout the year.

If this is the first time you have owed a penalty, you can also ask for an abatement or administrative waiver.

Abatement https://www.irs.gov/businesses/small-businesses-self-employed/penalty-relief-due-to-first-time-penal...

Note that interest on late payments can't be waived or abated.  If part of your bill from the IRS includes interest, you will be stuck with that, although if you apply for an abatement on the penalty part, it may result in the interest due being recalculated.