The likely reason is because of social security taxes. Social security taxes are capped at a maximum of $7,347 per taxpayer for 2016. When you are entering both W2s under your name, the program is reading them as both yours, so this is likely causing your total social security taxes withheld to be too large.
You then are issued a refund for these social security tax overpayments on line 71 of your Form 1040. So, this is likely why you are seeing a larger refund under these circumstances. Obviously, this is a refund you don't want and why it is important to correctly separate the W2s as it will generate an IRS notice if it was not corrected during the review.
