Bee:
1) Yes, you ARE still exempt from FICA taxes for the Feb 08 - Sep 08 period even if you file jointly. See link below:
Nonresident Spouse Treated as a Resident
Hence, even with only ONE W-2, you should NOT owe FICA taxes for this period.
Contact your employer and show him pages 48-49 of IRS Pub 519 (which can be downloaded from
Internal Revenue Service) and ask that these improperly-withheld FICA taxes be refunded to you.
2) First, try to get the
employer to refund the FICA taxes as noted above. If that does not work, delay filing and submit IRS Form 843 to recover the improperly-withheld FICA taxes
FIRST. Once those taxes are recovered, then file jointly with your spouse.
If you have a joint refund due, you have until 15 April 2012 to file the return to recover the refund.
If you OWE money, file Form 4868 to request an extension until 15 October 2009, and submit a payment with this Form 4868 to cover whatever you would owe.
3) You can file jointly with your husband and CHOOSE to be treated as a resident alien for all of 2008. In doing so, however, you would make recovery of the improperly-withheld FICA taxes problematic.
You can file separately from your husband and file Form 1040NR or 1040NR-EZ as a non-resident alien, which will allow you to file Form 483 to claim a refund of the improperly-withheld FICA taxes.
It is impossible to determine which is the best option at this time, as I do nont know how much you or your husband has earned in 2008, nor in which state you currently reside, nor from which country you originate.