This year is a complicated one for me for tax purposes. I've been in the US since mid 2015, with F1 status. I currently still have F1 status, with OPT.
If I've understood everything correctly, I passed the substantial presence test for tax residency last month in July. Does this mean that I am a tax resident in 2020 from July onward, or for all of 2020, or from when I first entered the US this year (I've been in the US for pretty much the entire year, except that over the new year break I was in Canada, and returned to the US on Jan 3)? In particular, next year, for 2020, should I file as resident or dual-status?
My employment this year will have been as follows. Jan-Apr: I worked for Employer A. Jun-Dec: I will have worked for Employer B. Employer A did not withhold FICA taxes, because I was a non-resident on F1. If I file as a resident, will I need to pay these taxes at tax time next year?
In July, I got married. My wife is a Canadian citizen. By the end of this year, she will have been in the US for about 5 months, from August onward. For 2020, will we be able to file jointly?
You are a resident alien for all of 2020 (or, at least, starting from Jan 3).
I don't believe there is any way to pay FICA taxes on your income tax return. You can notify the employer, but it would be them who would need to pay the FICA taxes to the government, and then they can seek reimbursement from you somehow.
By default, she is a nonresident alien for 2020 (assuming she hadn't spent significant time in the US in 2018 or 2019). Nonresident aliens cannot file jointly. However, you guys can file jointly if you choose to use the Nonresident Spouse Treated as Resident option, which makes both of you into resident aliens for the whole year, and requires you to file jointly.
Note that making her into a resident alien for all of 2020 would subject her worldwide income for all of 2020 to US taxes, although she may be able to use the Foreign Earned Income Exclusion (using the 12 months before she came to the US) and/or the Foreign Tax Credit to reduce the tax on her foreign income. So you would have to balance the tax benefits of filing jointly (which likely has a lower total tax than filing separately) against the complexity of dealing with her foreign income on US taxes.