I completely agree, I find this very annoying and it is still happening as at v 2018.2. I think it happens for suppliers that you have ever used Pay Bills for instead of Spend Money. Don't get me wrong, I think this is a fantastic idea to warn people if I do owe money to the supplier however to me anyway, it is a no brainer to only bring up this warning if the Pay Bills balance for the supplier is non zero.
If I record a purchase for $100 to XYZ corp and then later I am paying money to XYZ corp in Spend Money then it just makes sense to check if I owe any money to XYZ corp and then warn me. In fact it's a great idea because it may be that I should very well be applying that payment to the bill.
However if I don't currently owe any money to XYZ corp (even if I have recorded purchases to them in the past), then don't do the warning, it really gets annoying after the 100th time. This would surely would be an easy fix?