An EU ETS factsheet says:
A business is penalised if it does not surrender enough allowances. It has to buy allowances to make up the shortfall, is “named and shamed” by having its name published, and must pay a fine for each excess tonne of greenhouse gas emitted. In 2013, the fine amounted to €100 per tonne of CO2 (or the equivalent amount of N2O or PFCs). The penalty rises annually in line with the European consumer price index.
Where does this fine money go? Does it go to the member state like the primary auction money, or does it go into some EU budget?