There are some instances in which the Form 5329 is not required to be included with your return, even if an amount is appearing on Form 1040, Line 59 for Additional tax on IRAs, other qualified retirement plans, etc. This is why Line 59 states, "Attach Form 5329, if required."

Per the IRS Instructions for Form 1040, page 50:

Line 59

Additional Tax on IRAs, Other Qualified Retirement Plans, etc.

If any of the following apply, see Form 5329 and its instructions to find out if you owe this tax and if you must file Form 5329. Also see Form 5329 and its instructions for definitions of the terms used here.

1. You received an early distribution from (a) an IRA or other qualified retirement plan, (b) an annuity, or (c) a modified endowment contract entered into after June 20, 1988, and the total distribution wasn't rolled over in a qualified rollover contribution.
2. Excess contributions were made to your IRAs, Coverdell education savings accounts (ESA), Archer MSA, health savings account (HSA), or ABLE account.
3. You received taxable distributions from a Coverdell ESA, qualified tuition program, or ABLE account.
4. You were born before July 1, 1946, and didn't take the minimum required distribution from your IRA or other qualified retirement plan.

Exception. If only item (1) applies and distribution code 1 is correctly shown in box 7 of all your Forms 1099-R, you do not have to file Form 5329. Instead, multiply the taxable amount of the distribution by 10% (0.10) and enter the result on line 59. The taxable amount of the distribution is the part of the distribution you reported on Form 1040, line 15b or line 16b, or on Form 4972. Also, enter “No” under the heading Other Taxes to the left of line 59 to indicate that you don't have to file Form 5329. But you must file Form 5329 if distribution code 1 is incorrectly shown in box 7 of Form 1099-R or you qualify for an exception, such as the exceptions for qualified medical expenses, qualified higher education expenses, qualified first-time homebuyer distributions, or a qualified reservist distribution.