You are considered resident aliens if you pass the substantial presence test OR have a green card. If you pass the substantial presence test, you are a resident alien even if you are not in the US legally, or you are in the US legally on a temporary basis but not authorized to work. (The IRS does not inform to immigration if you are working without authorization, they just want their money.)
https://www.irs.gov/taxtopics/tc851
If you were in the US for at least half of 2024, you pass the substantial presence test and it is fine to file married filing jointly and use Turbotax. How you filled out your W-4 does not matter, that is just used so your employer can calculate your withholding. If you had excess tax withheld, you will get a refund.
