You are correct that you don't qualify for the credit for excess SDI withheld by one employer on your tax return, but only when there are multiple employers. See this thread for a discussion of this topic.
If you received two W-2s from the same employer, same EIN, you should only enter one W-2 for that employer. If one of the W-2s is marked as a Corrected W-2, enter the information from the Corrected form in TurboTax. When you are finished entering the information, a screen appears, "Let's check for uncommon situations". Check the box, "W-2 was corrected by my employer (Form W-2c)" so that the IRS will match the information on your tax return with the correct form.
See this article for more information on Forms W-2.
If the employer didn't issue a Corrected form, and your federal wage info in boxes 1–14 is the same (or blank on one W-2), and the state info in boxes 15–17 (or local info in boxes 18–20) is different, you’ll enter both on the same W-2 screen. Enter all the info from the most complete W-2, then enter the different state and local info from the other W-2.
See this help article for more information.
If you have questions regarding the reason two forms were issued, contact your employer.
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