I think we must clarify things and what "it" is
(1) Giving tax break is what Belgium wanted to do. Belgium offered aid, companies took it.
(2) The fact that said tax breaks (or aid) were illegal is the violation of the law that someone is supposed to pay for.
Belgium paid for (1), of course, that was it's intention. But it does _not_ pay for (2): it actually gets it's money back because of (2), if I understand correctly. Or this money goes back directly to EU, this is not important; anyway, Belgium is not losing money because of (2), companies are.
So, companies are paying for performing action that was completely legal in the law of the country they were operating in. Companies are paying for Belgium lawmaker's mistake.