I am a sole proprietor of a small business started in 2016. I wanted to keep my business as separate as possible, so my wife completed our personal returns yesterday without including my business information. Today we are trying to complete a return for t

[bwa]

What your wife did was incorrect.  You cannot keep your sole proprietorship separate on your personal tax return.  The personal tax return must include all sole proprietorship and personal income and deductions.  Now, unfortunately, you can't complete a new return for the proprietorship.  Rather, you need to amend your original return to add the proprietorship there.

In the future if you want to keep them on separate returns you would need to incorporate the business.