The program will ask you the same questions for each identical type form you enter. So every time you enter the 1099-R and indicate that it is a 401/457, you will be asked the same question. This is because a lot of times things apply specifically to that source of income. Ex. If your getting a pension and a spouse is getting a pension, then you would both need to be able to answer the same questions. Or if you are having xyz withheld from pension A and similar but different wxy from pension b, you would need to opportunity to enter all of that.
If you entered the same health insurance premiums both times, then this would be the problem. The program will not catch this as it has no way of knowing what your actual premiums are. You would need to go back through and delete the information about your premiums in one of the 1099-R's. This will lower your refund, but it will not be duplicating a deduction for the same premiums.
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