I don't think this is a conflict. Once the legal order is made and delivered to the company, the NSA receives a real-time feed of that user's data going forward (and all past data) and uses Prism to pull all the disparate data sources together for the analyst to analyze.

Surveillance isn't just about receiving your past activity and data that already exists - they want to watch suspects use these systems to communicate in realtime to find out who else they are talking to.