I've experienced this very same problem. I don't know if the dock icons misbehaved after "a couple of hours" or it's merely that I didn't notice they were misbehaving until I clicked on them, but some of them certainly pointed towards random documents.
What I did notice immediately after the restore is the Apple menu items (About This Mac, Software Update..., System Preferences) all pointed to random files. For example, Choosing "About This Mac" would open the "About This Mac" window fine, but clicking on "More Info..." would attempt (and fail) to open an obscure jpg buried in an application package. To correct this I deleted the jpg, clicked on "More Info..." and after it linked correctly I restored the deleted file.
I restored my OS X volume a more than a week ago and I'm still finding incorrect links. Just today I clicked on the "Address Book" icon in the dock and it launched a random unix file in the Terminal window. Not good.
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