I think that's a good point halogenic. For an amateur, the most instructive moves in a master's game are most likely the ones not being played (and the reasoning behind why they're no good). This is where the analysis Estragon mentions comes in handy. Also a coach or stronger friend can help. For a book, consider Chess Master vs Chess Amateur, where you can see how bad amateur moves are punished in real games against masters.
I would in fact recommend against master games when trying to do your own analysis. What you do want from them is the pattern recognition you're talking about. I agree with estragon on using the quick viewing method just to get a feel for how the game progressed after the opening. E.g. lets say you pay through a few games a day, and notice white often attacks on the kingside with pawn play... or that black often pressures the center with pieces (and some standard maneuvers for doing these). This is probably the most beneficial way to review master games on your own, answering those two: generally where and generally how.
With a coach, friend, or book to guide you though, you can try to do some of your own analysis first... and them compare notes with the coach, friend or book in order to learn.
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It stood out to me when you asked "how to refute or play aginst inadequate moves." I think this is an interesting topic. In short, learn positional play and endgames to refute the really ugly ones.
But even further, when experienced players try odd moves, they can really test our chess understanding, logic, and analysis skills. Sometimes "ugly" moves are chosen for practical reasons such as the clock or psychology, and has recently been an interesting line of thought for me (when and how to choose the "right" ugly moves :) I feel like this deserves its own topic.
Let me say up front that I am an amateur player. Like many amateur players, I want to improve. So here I was making plans to create a regimen of study to improve my play and I was considering studying the games of the masters. It has long been held that studying the games of the masters increases your pattern recognition, which in turn increases your positional instinct, so to speak, in your own games. I have some questions for you masters, instructors and experienced players out there regarding the supposed benefits of increased pattern recognition. Firstly, the majority of the patterns that my subconscious mind will be subjected to when I study master level games arise primarily in master level play, correct? So then, when either my amateur opponent or myself makes a positionally unsoud move or, as is often the case, more than a few such moves, how does studying the patterns of those who do not make such mistakes benefit me in my own games. Even suppose that only my amateur opponent makes a positional mistake, how would my increased pattern recognition enable me to refute such a mistake when these same mistakes are not found in master games? What percentage of the patterns I'm studying can realistically be expected to arise in my own games versus other amateur players who are equally inept at master level positional play? In order to get the most out of studying master level games, shouldn't I be playing against masters? Is there a book or other resource that teaches how to refute or play against such inadequate moves? Please, if you choose to answer one or more of my questions, don't just give a pat answer without any explanation. I appreciate all of you who took the time to read my post and who offer as best as you can, answers to my questions.