Just about to add 'Source Code' (BD) to my collection, it has the same UPC as the double disc version, but mine has only a single disc.
My question is, do I enter this as an alternative issue, even though everything else is identical, apart from the number of discs? I have several movies like this, especially Blu Rays.
As Addicted2DVD has mentioned, it is nearly always the disc with special features on it.

Aside from a special features disc, another difference I've seen in one instance (and I'm betting there are other cases) is when a Blu-ray/DVD combo is re-released with the same UPC without the DVD. I'm not talking about secondhand Blu-rays omitting the DVD, which is very common, but an actual re-release.