My taxes withheld only covered 88.6% of my tax liability for 2024 not the 90% minimum required; yet TT didn't calculate a penalty. Is there a problem with the TT program?

There is no penalty if the amount you owe is less than $1,000.

There is no penalty if your withholding is at least 100% of your 2023 tax liability (110% if your 2023 AGI is over $150,000 ($75,000 if married filing separately)).

@rjs thanks for the reply. Unfortunately I owe over $3000 for 2024.  My AGI is over $159,000 and I fall $546 short of meeting the 110% minimum of my 2023 tax liability. 

If you are using the desktop TurboTax software, switch to forms mode and open Form 2210. Go through Part I line by line. See if the numbers are right, and if it tells you not to file Form 2210.