Why won't some apps download from iCloud?

[iMore Question]

I had an iPhone 5c and just upgraded to a 6s the other day. I've never really used iCloud before, but the guy at Verizon told me how I could transfer everything from my old phone to new one with iCloud. I backed up my old phone to iCloud..then set up my new one with it. The only issue in having is a couple of the apps would just be blacked out and weren't downloading back to my phone. I tried going to the App Store and downloading them again but then all my stuff was lost! How do I fix this?