Bio-fuels are supposedly carbon neutral, although there is some debate about this as it's only really true if you keep growing plants at the rate that you're burning things
The cost to refine bio-fuels so they are suitable for use is very high
Growing crops specifically for bio-fuels may mean there isn't enough space or water to meet the demands for crops that are grown for food
In some regions, large areas of forest have been cleared to make room to grow bio-fuels, resulting in lots of species losing their natural habitats, and the decay and burning of this vegetation also increases carbon dioxide (CO2) and methane emissions