Sinister 2 (2015)

In the scene where the actor throws something at a bowl in the attic and a rat scurries out from under the bowl, trainers were off-camera and gave him peanut butter to keep him in position. The AHA Safety Representative checked the area to make sure the area was safe, clear and all escape routes were closed off. The rat was never under the bowl. They started filming the rat after the bowl was flung away. 

In the scene where the spider crawls onto the porch near the boy, the trainers brought the spider to the area in a container. Prior to filming, the trainer placed the spider on the porch, allowing it to crawl on the edge. At cut, the trainer placed the spider back in its container. 

In the scene where the rats crawl all over dead people in the church and crawl out of their dead bodies, most of this scene was accomplished in post-production with CGI. However, a portion of the scene was live action. The trainers brought the rats to the set and placed food on each of the actors lying on the ground. The actors were prepped on the scene so were not alarmed to feel the rats on their bodies. The director took several shots of the rats sitting on their bodies.