Congratulations to those who worked on this case. Puerto Rican cases, as with other small island-based (or otherwise isolated) populations are very difficult to solve because when you go out about 5-6 generations out on the family tree just about every person on the match list has 2 or more sets of common ancestors with almost everyone else on the match list. Just because you've identified a set of common ancestors for two persons who match the doe, it doesn't mean that they are ancestors of the Doe.
Even if you rely only on triangulation - (i.e., identifying two persons who share a common segment on the same chromosome as the Doe), those two triangulating matches may have more than one set of common ancestors.