I had the issue with both Aperture and iWork. If you call 1-800-APLCARE and ask for the Aperture team they will help you out. The Aperture representative told me that they are aware that this has been happening and he happily issued a redemption code, after which I had to delete the Aperture app and then reinstall it from the App Store.
The iWork issue is a little more complicated. If you skipped any operating systems - if you leapfrogged over Mavericks, say - then you're stuck in a weird zone where nobody knows what to do. The representative admitted that the free upgrade to iWork was only free AND automatic if you were in Mavericks. I'm not sure if that was accurate or not, but that's what she said to me. But, if you still have the original install DVD and you give them the product numbers off of it, they can validate you for a redemption code. It was rather an unusual process, and since I didn't have an installation DVD in my hand, I just looked up the product numbers and they said, "Close enough". It was a weird thing, but I did get the code.
Really, if you're dealing with Apple products, the only way to resolve it seems to be to call. It seems like whatever hook they use to drag their products into App Store licensing in a way that Yosemite can understand is not functioning perfectly. If none of the other solutions worked, call! it worked for me.