American marines in Haiti are being threatened with punishment (extra duty, confinement to barracks, etc) if they do not take their anti-malaria pills (doxycycline). This drug works, but it has some side effects (digestion problems and additional skin sensitivity.) This sort of thing (troops not taking care of themselves) is not a new problem.
In past wars, troops were ordered to do certain things to keep themselves healthy, and commanders faced similar problems with non-compliance. Some of these problems still exist, like taking your malaria medication. Malaria is a debilitating (and sometimes fatal) disease found in most tropical areas. The medication to prevent it has always been unpleasant, either in terms of taste (no longer a problem) and side effects. These uncomfortable side effects are the big problem now. Sometimes it's a huge problem. Last year, PTSD (post-traumatic stress disorder) was found to have unexpected side effects. It was discovered that a widely used anti-Malaria drug, mefloquine, caused anxiety and suicidal thoughts if taken by someone with PTSD. Once this was discovered, troops with PTSD could no longer use the drug. This impacted a lot of troops, and prevented them from being sent to some areas (like the Persian Gulf and Afghanistan) where Malaria is a risk. The number of troops affected was considerable. In some parts of the world, less effective drugs, like doxycycline, could be substituted. But for doxycycline to work troops had to take the pill daily, without fail.
In combat, the troops are stressed and have a lot of things to do, all the time, and often under fire. Lack of sleep creates constant fatigue. So commanders had to accept the additional casualties from troops not using water purification tablets (to avoid drinking water that would make them ill), keeping their feet dry (to prevent skin conditions), wearing their cold weather clothing correctly to avoid frostbite, or drinking enough water in very hot weather to avoid heat related illness, and so on.
But when there is not a lot of shooting going on, as in Haiti, or with combat support troops who are not under fire most of the time, you are expected to do what you were ordered to do to avoid illness or injury. And that's what's happening to the marines in Haiti.