No, they haven't yet.
They did offer apologies for their role in the assasination of Patrice Lumumba.
Well no. Not for what happened in the Congo Free State under Leopold II.
There are multiple reasons for it but one of the most important is that it only became a Belgian colony in 1908 and when that happened most of the violent practices that happened in the Congo Free State ceased to exist. Not saying it suddenly became a paradise but in general the Belgian Congo was not the worst place to be if you were in sub-saharan Africa.
A lot of people seem to refer to the Congo Free State as the Belgian Congo. That's is simply wrong. The Belgian government had no say in what happened in the Congo Free State.
*Flemish?