I know I have said variants of this already a kazillion times in this weblog, but the most chronically annoying thing about sociology is the ease with which sanctimony and moral posturing are allowed to stand in for the actual work of evidence and argumentation. To be a sociologist is to regularly be in a room where things are taken for granted that are actually minority opinions even among social scientists. Which is not to say that sociologists are wrong, necessarily, but it would probably be much healthier if there was more disagreement and more forcing people to articulate good arguments for things that are instead matters of tacit agreement.
The second most chronically annoying thing is how much shoddiness there is, which I think has a variety of causes, one of which is that the breadth of the discipline leads to an extreme sparseness of researchers engaging any particular topic. Sociology has a large number of really smart people who seem like they are mostly off on their own--if I was at all confident about the "really smart" part, I would suppose I am one of them--which is bad because the history of intellectual thought shows plainly that even the smartest people go wildly wrong if they don't have a community to provide reaction and discipline for their thinking. If you were going to design an intellectual environment ripe for the making of cranks, there are certainly worse structures than exactly that of contemporary sociology. I've lately taken to referring to sociology as "the lonely science."
Update, next day: The first paragraph above might be taken as suggesting that I am against "activist" oriented research. I'm not. Quite the opposite. I think it's a great thing when research has implications for activism and have no problems with research motivated by an activist impulse. Not much of my own work has exemplified either, and I take that as a legitimate knock against my own work. The problem comes when the determination to tell some high-minded story crowds out careful work and reflective attempts to understand what is actually going on with what one is studying.