This is because the act of approval to the UPC agreement substantively amends the constitution. Such changes require the approval of the Bundestag, which needs a 2/3 majority to pass significant amendments.
More specifically, the Second Senate of the Federal Constitutional Court stated that an act of approval to an international treaty that has been adopted in violation thereof cannot provide a democratic legitimation for the exercise of public authority by the EU or any other international institution supplementary to or otherwise closely tied to the EU. This is because the process of European integration by democratic means also entails the right of citizens that sovereign powers be conferred only in the ways provided for by the Basic Law.
The German Federal Constitutional Court has provided a detailed summary of the case in English here.
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