90% of the time, when I dislike a commercial "craft" beer, I find the same three problems wrong with it:
1. Not enough hops. The beer will be called "IPA" or even "Pale Ale" and it will be clear that they went cheap on the hops and brewed a bitter, malty beer with little discernable hop flavor or aroma. I understand that hops are both expensive and hard to come by for a smaller brewery, and that IPA is such a big part of the market here that you pretty much HAVE to have one to make it as a small brewpub, but this causes me to try the IPA or DIPA last when I visit a new brewery.
2. Too much suspended yeast is left in the beer. This will cause an odd texture, muddy flavor, occasional harsh bitterness, and (for me) painful bloating.
3. Poor water chemistry. I have had a lot of bad beer in places I know to have very hard water (where local homebrewers I know will universally use RO water). Inevitably the pale beers have a harsh, acrid quality that I can't get past. Then I know other breweries that have the benefit of very soft water who just add enough gypsum to get 50 ppm calcium and double the amount for their IPA. They aren't necessarily any better of water chemists than the guys with the nasty water, but their beer will taste a hell of a lot better. So the lesson is to avoid putting a brewery where the water's no good for brewing.
Very occasionally it is something worse, like a hop-forward amber ale that is just roasted barley and 2-row tasting like a hoppy ashtray, or a pilsner that tastes like diacetyl and suspended yeast... but 90% of the time that a craft beer tastes bad, I find it is one of the three above-listed reasons.