Have microorganisms manipulated by human scientists working for the military, contaminated the planet and contributed to human suffering?

This is true. There has been much germ warfare research. There has not been extensive success by human scientists to greatly increase virulence of many microbial species, but there are some that have been genetically modified to worsen their pathologic effects and these are in the environment through reckless testing in the field, so to speak, and occasionally used on human targets as a part of clandestine operations to gain a military advantage. These have not spread widely and are not currently the cause of any epidemic level outbreaks, but the potential is always there—when the right conditions are present, it can happen.