I arrived to the US in Aug. 2006 on an F-1 visa. I went from a bachelor's program to a master's now... still on an F-1 visa.

I take it that I was a resident for tax purposes in tax year 2011 (due to substantial presence test), but did not have FICA withheld.. (I worked 6 months CPT, full time).

Was the FICA incorrectly not withheld in 2011?

Thanks in advance!

You should have informed your employer that you are nonresident in 2011.
Now make sure that taxes are withheld in 2012. Send them email.

So how will this effect my 2011 tax return? Will I owe FICA to the IRS?

If IRS finds out this, they will ask your employer to pay this. Then your employer will contact you.

Actually, you WERE liable for FICA taxes for 2011, since 2010 was your FIFTH year under the F-1 visa.