If you enter W-2's from different employers and they withheld too much social security tax, you should get a refund of the excess on your tax return. It is possible that the IRS considers your employer to be one since they appear to have common ownership and that could be the issue.
You could try entering one of the W2's without the ID number and see if that resolves the issue. If so, you could file the return manually without issue.
You could also try deleting the two W-2's and reentering them.
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