I got married and forgot to change my name with SSA. My new employer has my married name on W2 but we are now separated.

You do not have to change your name with the SSA to file. However, you have to use the name on your Social Security Card. That is what the IRS will match to your Social Security Number.

Since my most recent W2 has my married name, will it create a mismatch (because the name on SSC does not match the name on the submitted W2)?  I would hate to create some sort of red flag.

If it did create a mismatch, when you attempt to e-file, it will be rejected and you could then go in and change the name to correct it. Just make sure you check on the status or watch for any emails.