TTX will pay interest and penalties if it is shown their calculations were wrong, but that doesn't cover anything you entered in the wrong spot, or didn't enter at all.
Read the letter closely to see what they claim you missed ...not the taxes owed....the income areas, or credits claimed by you that they disagree with..
One simple error that people sometimes make is if the miss-assign 1099-R income to the wrong line and the IRS doesn't notice it's actually being reported....just one lien off (line 15b vs 16b on a form 1040)...and informing them of that takes care of it.
But if something else, you need to see where the problem is, see if you agree......."yeah..missed that" and pay up, or disagree and explain why they are wrong.