Benigna Didn't Kill the Orphans, and they didn't kill Tomas
I just watched the movie and it became apparent to me that Tomas and the Orphans were killed by the head and staff of the orphanage, seeing in the super8 films how they mistreated Tomas, they must have reached the point that they were fed up of taking care of him and just killed him by having him drowned in that cave, the orphanage staff must have put the blame on the orphans instead, telling the police that it was their prank that caused Tomas' demise,
of course the children knew that this was false, and probably thought that this hidden boy was killed by the staff themselves, it was left uncertain whether the orphans really did find out about Tomas when he was alive or that his existence was only revealed to them when he was killed, now the staff knowing that the orphans had suspicions on who killed Tomas, they killed the orphans themselves by poisoning them, leaving no traces of their murder, this was convenient because logic dictates that it would have been the vindictive mother Benigna who would have those orphans killed in the presumption that it was them who lead Tomas to his death, but I don't buy that, they killed the orphans themselves to erase any trace to their crimes, if the staff were truly innocent I doubt they would have let those orphans not receive a proper burial, I seriously doubt Benigna could have placed their bodies there, even if we assume she did kill them, there's no way the staff of the orphanage would not cater to the corpses of those orphans, and there is no way for Benigna to keep the staff in the dark and had those bodies tucked away in that small cottage, no, I think the staff and management put those bodies there themselves, assuming that the police had verified the murder of the orphans, the orphanage staff would have the responsibility to bury those children, which they did not, probably because they didn't want to pay the expenses of burying them, Benigna probably knew where those children were buried, and went to that shed to possibly take the remains and give them a proper burial, seeing the orphans to be much of the same victims as his son was.