So, basically you believe that people are gaming the system but you have no examples of how this happens or which companies might be doing this?
Anyway, the article's argument is that the certificates for renewable energy are created in e.g. Norway and Switzerland where it is easy to produce cheap hydropower which cannot be transported to Germany. Meanwhile the Norwegian and Swiss do not buy energy with certificates because they "know" that their energy is clean.
This is indeed true and a valid argument. However Norway and Switzerland produce only a finite amount of these certificates. If demand for certified green energy does not exceed this supply then this is simply a sign that not enough people are willing to pay extra for certified green energy which is regrettable but not a fault of this system.