As they leave the bakery Root tells Reese that she has taken Jacob's ammo for them to use. However Jacob's weapon is the FN P90, chambered in 5.7 x 28mm. Their weapons are H&K pistols, chambered in either 9mm or .45 ACP, which are completely incompatible.
The major selling point for Samaritan, as is often repeated, is that it remains in the control of a private company, which gives the government plausible deniability. However, as suggested by the name, plausible deniability means that a person or organisation can plausibly deny having any knowledge of the actions in question.
The only way anyone would need to deny anything was if the public found out that there was an entity with access to everyone's personal information and communications, at which time the only thing the government would need to deny is knowing Samaritan access to that information, while also being the only people who could have given it that access. Being able to deny accessing the information personally, and having no part in processing it, is not enough to keep anyone out of prison, particularly when they were apparently willing to admit to acting on illegally obtained information.