Toxins
There are certain plants that can cause a negative reaction with a matoran system, just like here on earth. Some can give them a mild hallucination while others will leave the Matoran bed ridden for days as it is work out of their system. Which plant is which I'll leave that for the M/U inhabitants to figure out. Probably would name the plants something unpleasant and are easily avoided.
Not all of the Toxins needed to be ingest, some are inhaled, or are injected. These are what should truly be feared. The breath of a doom snake will turn your insides into liquid soup. While the type of venom that affected Tahu Nuva prevents the digestive system to produce energy. Its the venom and toxins that provide the most danger for these beings, especially since there are few remedies to them.
Mutations
As far as I've know, there are Two types of mutations in the M/U. mutations that can be reverse, and those that can't. And unless their deformed body is caused by a hic up while being created,those who have been mutated are often shunned.
Hordika Venom: This is one of the few that can be reverse if caught in time. It turns sentient beings into half rahi versions of themselves. Eventually the Rahi within will overtake them, leaving nothing more then mindless beast.
Energized Protodermis: The ability to transform, or destroy. In most cases the resulting transformation are often noble. However we must feel pity for those results that turns out worse then when they started.
Experiments: Those who were captured by beings to be used as test subjects don't often survive the experience. However those who do are forever changed. And the Makuta do have a way to yield interesting result...