Popper was arguing against the conspiracy theory of society: the idea that bad things happen because some sinister group of people actually plans disasters. For example, the great depression was produced deliberately by greedy capitalists because buy more raincoats when they don't have a job or something. Popper claims the conspiracy theory of society makes no sense because such conspiracies hardly ever turn out as intended.
Sometimes people really do plan to do terrible things, e.g. - the Nazis and the Soviets planned to murder millions of people. But they usually fail to carry out their plans fully according to Popper.
I think this argument falls down because people do try to do evil stuff and often partially succeed, so sometimes it is appropriate to accuse some person or group of arranging some bad event. Popper doesn't explain when such attributions make sense and when they don't.
A better explanation can be found here:
The problem isn't just a problem with saying that a person wants to arrange some bad historical event, but with saying that he wants it for some secret bad reason. The problem with such theories is that they don't explain what actually happens. Since the motives of the conspirators are supposed to be secret, they are supposed to act exactly as if they believed their stated motives. As such, the alleged reason for the conspiracy plays no role in explaining what actually happened.
In addition, there are problems of how to arrange the conspiracy and prevent people from defecting in secret. For example, if somebody had offered the members of the Warren commission a bribe to say Oswald killed Kennedy, then what would happen if the briber didn't pay up? Would Warren have gone to the police and complained that he didn't receive his bribe for covering up for a murderer? And how could the conspirators who approached Warren and the other members of the commission know they wouldn't go directly to the police?
Saying Hitler wanted to kill the Jews and that the Soviets wanted to kill capitalists isn't a conspiracy theory in this sense because they openly said they wanted to do that.
It may be the case that some Marxists hold a conspiracy theory about capitalists wanting to oppress workers despite the lack of an express intention to do so. I'd guess many Marxists are more in the category of not understanding the economic objections to Marxism pointed out by economists such as Bohm Bawerk, and the moral objections to their ideas explained by philosophers such as Ayn Rand.
Others ideas that are commonly considered conspiracy theories should be considered on a case by case basis. The mere fact that a person is suspicious government or doctors or environmentalists doesn't have any bearing on his rationality or lack thereof.
There are a few other books on conspiracyn theories that are interesting but not officially categorised as philosophy, such as 'A culture of conspiracy' by Barkun and 'Conspiracy: How the Paranoid Style Flourishes and Where it Comes from' and 'The Hidden Hand: Middle East Fears of Conspiracy' by Daniel Pipes.