It seems to be spelled out pretty clearly. The NSA was collecting internet messages through ISPs. These messages were supposed to be to, from, or about specific non-US targets, and the systems were supposed to have "minimization procedures" that would keep them from collecting other messages that were to/from/about US citizens. These procedures were found to be insufficient: the NSA collected tens of thousands of messages about US citizens without their consent, which the court found to be in violation of the fourth amendment.