The Columbian Exchange generally worked to help Europe and to hurt the people of the Americas. The main bad effects of the Exchange were felt in the Americas.
There was, at least arguably, one really bad impact of the Exchange for Europe. This was the fact that tobacco came from the New World to Europe. Though people did not know it then, tobacco is very bad for them. Therefore, it would have been better for Europeans if tobacco had never made it out of the Americas.
However, that is a relatively minor thing. The really negative effect of the Exchange was felt in the Americas. This was the coming of infectious diseases to the Americas. The people of the Americas had never been exposed to the kinds of infectious diseases that existed in the Old World. These were diseases like smallpox and the measles. Because the natives of the Americas had no resistance to these diseases, they died in huge numbers (some scholars believe up to 90% of them were killed) when the European germs arrived. This was, by far, the most important negative effect of the Columbian Exchange.