It sounds to me like the adventure was well written and shouldn't be a problem. Just because a monster is an an adventure doesn't mean the characters have to kill/defeat it. Throwing in the occasional powerful beastie lets the PCs know the world doesn't revolve around them, and that if they press their lcuk, bad things can happen because for the most part the gods (DM) won't overly protect them. I know D&D is combat heavy (which is fine), but there is also the assumption with a lot of people that if a creature is in an adventure, it is supposed to be/has to be killed. Part of this is seems to be due to the abstract nature of combat in D&D, but also the relative ease with which characters can defeat an encounter with a CR even with their levels or even somewhat above.
In some ways the CR system is nice to help a GM determine how tough a given critter is, but in other ways, the CR system has some problems. It assumes that PCs are all maxed out in equipment appropriate for their given level, but the determination for what is appropriate is given in relevance for a fairly high-magic world. I'm not trying to start anything here, but I have noticed that a lot of players and DMs assume that simply because a critter is CR whatever, that it is fair game for their PCs, when it might be more useful to take into account the individual strengths of the party when determining how tough an encounter is. So in some ways, the CR is somewhat misleading, not to mention the determination of a CR is never really detailed, so its a pretty subjective measurement that can have some major impact on the characters (XP and treasure-wise).
The other thing I have noticed is that some people seem to dislike the fumble rules some GMs like to throw into their games- I say to each his own, as long as the game is fun. I personally like fumble rules- they add an extra degree of uncertainty to the game and make combat seem more realistic (and I know its a fantasy game- but people do stumble and make mistakes in the midst of stressful situations, such as combat). I don't think fumble rules screw the PCs any more than critical hits do- the monsters are still susceptable to fumbles, just as they can still score critical hits. In fact, PCs have a big edge with critical hits compared with most monsters- most creatures use natural weapons that have a 20/x2 range, while PCs can tailor weapons for various situations. Also, since the DM makes WAY more attack rolls than PCs, the total number of monster fumbles should be much larger than the number of PC fumbles- and smart players should be able to find a way to capitalize on this.
Well, I degressed WAY off my original intent with this post.

I had been thinking about some game balance questions regarding CR and fumbles, I since they were brought up here, I guess this is as good of a place as any to ask what everyone thinks.