Although you "prepare" your tax returns jointly, you must NetFile each one individually to the CRA. Each return will receive its own individual NetFile Confirmation Number. If your spouse's 2016 tax return was not received by CRA, you should sign in to your TurboTax Online account, choose "Start or Continue my 2016 Tax Return", and follow the same steps you took to file your own return. If you prepared the returns in the version which you installed/downloaded to your computer, you will need to open up the 2016 program and proceed with NetFiling.
https://turbotax.community.intuit.ca/replies/2648037
