TurboTax does not automatically populate the amount you received for the 3rd stimulus payment - as you noticed when you needed to input the amount. Instead, it assumes your payment amount is $0 (since the box is empty until you populate it) and estimates the full amount included in your refund. When you complete the box with the amount you already received, it is merely removing that amount from your refund to properly reflect that you already received.
Depending on the W-4 you have on file with your employer, you may not be having the correct proportion of withholdings taken out anymore. There have been changes to the IRS withholding calculation in the last few years to catch up with the 2017 Tax Cuts and Jobs Act.
You can find the most recent version of the Form W-4 here. You can complete this and provide it to your employer at any time to update your current withholdings.
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