You're right, you can't Efile a W-2 with a negative amount in Box 4 for Social Security Tax Withheld.
What amounts do you have in Box 1, 2, 3, and 5? If you can clarify, maybe we can help.
You should reach out to your employer as to the reason for the negative amount. Maybe they withheld too much previously and are now showing a credit?
Here's some info from the IRS on Social Security.