Have a 1099 that does not appear on IRS wage and income transcript. how to report? tax year 2016

I received a 2016 1099 (long ago) that does not appear on my 2016 IRS wage and income transcript. Don't know why the company sent me 1099 but didn't file it with IRS.  I did receive the income and want to report it. Should I include the 1099 on my tax return even though it won't match my transcript? Could this cause a flag or something?  Only other thing I could do is report the income with my non1099'd income on line 1a...