About one of the only things you can count on in this world is change. However change in organisms doesn't always occur in a positive direction. Evolution is another word for change, and we know for certain that dramatic evolutions have occurred in organisms over time. An excellent species to examine the evolution of would be humans ourselves.
According to the Autism Society, the cost of caring for a child with autism can range from 3.5 to 5 million dollars over a lifetime. The cost annually for the U.S. alone is 90 billion dollars. This burden lies on the backs of parents, the insurance industry, and society as a whole.
People with autism deserve just as much right to exist as the rest of us, but it clearly can be seen that at least monetarily there is a cost and is just an example of how a change can effect other organisms negatively. Add to this the personal problems a person with autism has to cope with. The other problem with autism besides the daily struggles that must be dealt with, there is no known cause or cure for the disease so no one is quite sure if it is genetic or a mutation or simply a disease that can be inoculated against somehow.
It could be debated that since the disease can be treated, though not cured, that as a species we are trying to negate the negativity of autism so that would represent a positive change over all. Also autism, like Tourette's Disorder, is a non-contagious disease and so is less of a threat to the species over all. However, these diseases still represent a negative change in that people are suffering from these and similar diseases and cannot have the same level of enjoyment of life as the rest of society and require more than ordinary support to exist in society.
You could also make the argument that some organisms prefer and somehow defend against evolving. A good example of this would be viruses. All viruses work the same way and are unable to live outside of a host cell. All viruses use the host cell as a means of reproduction as well as shelter. Viruses do however change slightly in form and can seemingly adapt to some treatments. Many people would say that this represents a positive evolution, except that the original virus still exists and thrives. An example of this behavior can be seen with MRSA. MRSA is a type of staph infection that has become resistant to the common treatments of staph infection such as pennicillin or amoxicillin. The staph infections that MRSA has evolved from still exist and haven't been eradicated by the existence of a superior organism. So the change can be seen as neither good or bad, it's more of just a lateral move.
So you can see that some changes are bad and some are neutral along with the good evolutions that we have proof of. In the end, we can't really say if any evolution is a positive change until the end of time when we can tally up which species has done the best. And hopefully it will be us!