The Council can have a qualified majority vote - for the vote to pass 55% of the member states representing at least 65% of the EU population has to vote in favor.
The EU has a population of 450 million. 35% of it is a little over 157 million. Germany + France have a population of 149 million.
In practice every qualified majority vote has to have either Germany or France supporting the measure to pass the Council.
There are also Council votes that require unanimity. This is the so-called 'veto' that every country has. In that case obviously any country could hold up the process.
So, there are definitely places where things can be held up by a minority of countries, but I don't know if they can push things through. I think it would be more likely that they would leverage national level power for that.
