If you have three part-time jobs with W-2's, you may not have had enough Federal Tax withheld (or any) for the total of these incomes. Employers are not required to withhold tax under certain income levels, but if you have several of these incomes, you may end up owing tax.
With just your W-2's entered, you were eligible for a refund, but once you included your pension income, your tax went up. Look at your Form 1040 total income amount and compare it to the tax calculated and the tax you paid to see this.
You may want to increase the Federal Tax withheld on your pension, if this applies and you expect it to continue. This will cover any shortage in Federal Tax from your part-time jobs.
Or, you could file a W-4 at your part-time jobs requesting that tax be withheld.
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