Your tax due or refund is not "per W-2" or "per 1099R" -- the refund or tax due is based on the total amount of income you entered and on the total amount of tax that was withheld from those sources of income. When it all added together, you had a tax liability that exceeds the amount of tax you had withheld from your W-2's and retirement income. Going forward you could avoid owing next year by having more withheld from the W-2 income or more withheld when you take money from the retirement account(s).
https://turbotax.intuit.com/tax-tips/tax-payments/video-why-would-i-owe-federal-taxes/L3VXudPiN
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