They uploaded (AFAICT, lawfully obtained) evidence into their FBI-wide system, then it appeared in search results legitimately because there was a crossover with another investigation.

The whole point of criminal intelligence systems is to reveal these kinds of unexpected links isn't it?

Does the warrant get granted with some kind of limitations on how the material can be used or who can review it?

Obviously, they have done something wrong as they have apparently felt the need to send a mea culpa to the court, but I don't really see what it is.