We often get questions along the lines of “what is the difference between part x and part y?” with two items that appear identical at first glance. In this case, the Mini-Fit Jr 5557 series from Molex has a number of connectors that appear identical, but with different prices and part number designations.
If you look at the Molex listings for 0039013048 and 0039012040 it quickly becomes apparent that though the fit is the same on these, the first part number meets UL 94V-0, while the second one meets UL 94V-2 which is essentially a lesser version of the UL 94 standard. Hence the first part number is slightly more expensive. When in doubt, take a look at the manufacturer datasheet to find these differences when it’s not in the DigiKey attributes table.