@arunkesi We still need to know when you and your spouse first came to the USA with the H-1B and the F-1 ( as asked for my Super-User @mesquitebean . Were there other visits to the USA during the last five years? Which country are you from ? ( India ? )
Assuming that (a) you came to the USA early in 2018 and therefore passed the substantial presence test during 2018 with H-1 visa ; (b) Spouse has been in the USA with F-1 longer but has not finished the 5 year exemption period; and (c) you were married by the end of 2018 -------> you should have been filing a form 1040 as a resident for tax purposes; your wife , even though married , should have filed a form 1040-NR with filing status married. Even though I suspect from your post that both of you have SSN and therefore were able to use TurboTax to file a joint 1040 return, the above assumptions , if true, does not allow this.
You would need to amend your return using TurboTax and she would have to file a form 1040-NR ( not supported by TurboTax -- SprinTax, their partner supports this )
Please answer the questions asked or the answer may not be specific enough for your particular case
