If I overestimated the taxes I owe on my extension application and actually ended up with a refund, should I be concerned that this will cause me problems with the IRS.

No, it will not cause you problems with the IRS.  You will receive the refund that shows on your tax return.  If you paid taxes with your extension, make sure you entered the amount on your return, then the program will take what you paid and what you entered in your return and calculate the correct refund.

Thank you.  I was concerned about this triggering an audit or something.  I estimated that I owed a lot in taxes but, thanks to the new law, I ended up getting a refund.