The IRS tool works against the current year (2025) so if you only owed a relative small amount (hundreds) that same amount of income would have fewer taxes on it using the 2025 rates
I'd also suggest double checking your investment income inputs. Interest & dividends are taxed slightly differently than qualified dividends and capital gains/losses. If you skipped that part on your estimate, then you also would have shown that you would have a higher amount being withheld than if that income was part of the estimate.
To add the Vanguard/investment income, there is a section for "Other sources of Income" under which is "Investment Income". When you click onto that box, you get addition options for items like your interest/dividends/stock gains/losses/etc. The more accurate your inputs, the more accurate the estimate!
