I just take them as internal descrepencies. Since Bilbo wrote what we know as the Hobbit, there are going to be some mistakes and biased opinions. The stone giants could very well have been a different type of troll than the stone trolls he encountered earlier on his adenture. The term goblin is used in LotR as well, mostly for orcs from the Misty Mountains. And of course Bilbo's memory of the Elves of Mirkwood would have been more than a little biased considering the events that took place. The desert wyrms could very well have been a legend of Hobbits or everyone even.
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