As far as I understand, all member states have a veto in the European Council when it comes to questions of immigration and national security. The question of admitting refugees definitely affects both, at least to my layman judgement.
So why couldn't the V4 countries veto the proposal to suspend the Dublin system back in 2015? Doing so would prevent the quota system from being introduced in the first place since all EU countries would only be responsible for refugees that entered their country first.