It can depend upon your particular contract, but usually you might have two or more environments (I.E. Test, Dev, UAT, Production) and you would have a depot corresponding to each. Usually the depots are the same, it's really the license/SID files that differ. This has been my experience.
I mean that there is an option, at least when I have done it, within the Download Manager that asks something like "Do you want to consolidate duplicate files?" Something about whether you want to create an ISO from the download. It's possible that you made different selections at the point.
If you can verify that you answered the same to all the prompts in the Download Manager for both depots and the size is still different then I would definitely get with your sales representative so they can investigate why they are different.