The writers were all over the place in both movies trying to incorporate things from the books, while making them more Cruise-fitting. In the book, Reacher follows Sam to the diner, where she says she is a regular customer. Only later we find out her mom works there. Book Sam is a minor character (maybe 20-30 pages out of 400) and she's not a street kid, but lives, happily, with her mother.
Fighting a religious war is like fighting over whose imaginary friend is better.