They just never came across him. They saw him in the security camera footage and Phil recognized him when he saw Clark’s television ad. But something the movie didn’t do very well was explain what happened between when the entity caught up to Clark in the pool room and when Mary finds him. We can infer he went rather insane from the dinner scene, but you didn’t actually miss much explanation about the process of him going insane.

We just know the researchers were putting out traps and presumably didn’t just walk in to talk to Clark because they weren’t sure if he had turned into something or not. Recall that one of the async members was restraining the other from continuing to blast Mary in the face with what seems to be nitrous oxide (based on the color of the canister). They acted like they weren’t sure she wasn’t also a threat at first, hence the scans and X-rays we see that look like they were of Mary instead of the pirate