Why did my refund disappear when I acknowledged that I received both stimulus payments? I had a refund of around $1200 which turned into me owing $100 to IRS

Your refund "disappeared" because the amount of the refund the program was showing was a combination of stimulus were eligible for, and any refund (or in your case) tax due.  Once you indicated that you had already received your stimulus, it was removed from the amount showing as a "refund".  That left you with a tax due, the same amount that would have been on your tax return if there had never been a stimulus. The stimulus did not affect the amount of tax you paid or owe.  You didn't do anything wrong, you are not being punished.  

The way TurboTax chooses to give you your final result is not very pleasant.

What doesnt make sense is my refund goes from around 1000 to me owing 100. So the amounts don't add up as I am below the line of any deductions from the stimulus based on my earnings.