From rereading your post, it seems that when you enter both W-2s, the difference is that one service shows you owing $100 and the other owing $50. While I would expect them to be the same, there may be some variation in what you entered in the two websites.
As for entering one W-2 and seeing large disparities, there are so many variable about what you enter and the order in which you enter them, that it is probably not profitable to try to figure it out.
Your correct taxes will have both W-2s, so work only with that.
I do not know if you have copies of the 1040s for both services - you can see the 1040 on TurboTax even if you haven't paid for the product yet - but the thing to do is to compare the 1040s line by line until you find the discrepancy and see if the discrepancy can be explained by some variation in input (as it likely is).
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