Deforestation to make space for crops to be used as biofuels deforestation= destruction of habitat of animals
Instead of using space to grow crops for good the space is used to create biofuels
Loss of opportunities for research as land that can be studied and used to develop medicines is destroyed.
-Use a lot of carbon to extract fuels.
-Is it better to use for transport or food?
-Which industry should access it road transport, maritime, aeronautical... often its pushed for automotive but aero industry has less 'green' fuel options so potentially makes more sense to use it there.
If you consider alternative alcohol fuels, e-fuels, blended fuels etc. you can get a better picture for where and why we use each fuel for each type.