When reading books or articles on self-organization, they usually emphasize its amazing effects. Animals develop beautiful skin patterns, social insects achieve wonderful tasks with their hive mind and cities organize themselves despite of lack of central management. Much more sparsely, the more dangerous, negatives examples can be found. To give just a few: The principle of pulse coupled oscillators causes perodic cycle oscillators to globally synchronize even if the oscillators are only localla coupled. An example for this is the handclapping of an audience, but to some extend, also the synchronized regular military step of marching armies. On structures that itself can exhibit an oscillation behavior this can lead to the resonance disaster. In 1850, 485 french soldiers walked over a suspenion bridge in military step which led to resonance oscillations and finally made the brigde collapse; 226 soldiers died. Similar events happened in 1831 to Broughton's suspenion bridge and to Millennium Bridge in London (which did not crash, but moved heavily because of just 160 people). For this reason, the German Straßenverkehrsordnung contains a special paragraph prohibiting military step on brigdes.
Another example for unwanted self organization is the emergence of traffic jams from small disturbations in dense traffic flow. Assuming one driver has to break a little bit, this would cause the following car to come too close, the respective driver has to brake even harder to compensate. This means an even stronger decceleration for the next car and so on. On a global scale, a wave of stopped or slowed down cars can be observed running in the opposite direction of the traffic. Regulating the cars down to a lower speed limit can avoid the emergence of this problem and therefore increase traffic troughput depite to a reduced speed limit.
Finally, many of us experience another annoyance of an application of self-organizing complex systems. Social networks like facebook apply knowledge from network theory and data mining to extract information out of local social interactions. A user might not wanted to have disclosed this infromation in many cases. The problem is here that the robustness of self-organizing systems does not allow to fool the system. Even if you keep information like your job or your place of residence for yourself (or state it incorrectly), this information can be retrieved indirectly via an analysis of the information given by your contacts - Facebook knows you. So in this case there is only one solution - quit facebook! Even this step is difficult, Facebook normally offers only a soft deactivation of the account while keeping all your data. The function for deleting your account is well hidden: you might want to go to use the official form for deleting your facebook account. You are welcome.