Your original return and amended return are treated as two separate tax returns. You will receive the original refund that is owed to you based on the tax information you entered in on the original return.
Now you are adding missed income to an amended return, and it states you owe, which is not uncommon. When you are just reporting income on an amended return, the tax software will calculate the amount of taxes you should have paid based on that.
What you need to look at is the whole picture, what did you get back on your original return and what was owed on the amended return and see what it comes out to be. That is what you would have gotten if you had originally filed everything on the return the first time.
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