Investigation should begin with crimes that have occurred, suss out those circumstances where there is a bigger picture, and attain warrants for further investigation. Lack of probable cause means no search, a right extended by Amendment IV to all people (at least within US holdings as described above, which is where I think the FBI should be operating).
The fault here lies with Congress. FISA is their doing, and it expressly violates all clauses of Amendment IV. The FBI is at fault for swinging this particular bat in a room full of citizens, but they shouldn't have been given the bat to begin with. Why FISA hasn't had a Supreme Court challenge on constitutional grounds is beyond me, but IANAL.