I was under the impression they focused on him because he stopped the polygraph test, refused to submit DNA and they said he entered the lab area and a room Annie Le entered "soon after", whatever that means. If they think he's a suspect early on then any suspicious movements by other people in the lab will probably not be noticed, whereas movements by Ray would be scrutinized. They haven't said what tasks he was doing that weren't his, nor did they say if he put that equipment with her blood in a place that was not where it belonged. Nor did they say he moved stuff when they told everyone NOT to touch anything.
Why would law enforcement have been on the scene? The missing persons wasn't reported by her roommate until Tuesday evening. He had more than ample time to take incriminating evidence with him. Instead, we find out there's a whole lot of items left lying around for the police to find with his and/or Annie's DNA. I'm still not even sure how his pen would have fallen in that chase. If there was a struggle between him and Annie, and that pen was in his shirt pocket, it would have fallen out for sure. We haven't heard anything more about that green pen, like if there was any DNA or his fingerprints on it. Only that he liked using a green pen. We don't even know if that's totally true.
The problem with the card swipes is anyone can use a card. There's no password needed, nor is there a camera to show who's using it. Also, people can swipe to enter a room, but they don't need to swipe to leave. Whatever room Clark entered that Annie had entered earlier could have been empty. When he entered those other rooms he wasn't supposed to be in, was that within the space of 10 minutes? Or over the course of an hour? If the scanning into those other rooms was fairly quick, then I can see how suspicious that might be. Again, we don't know the nature of those rooms, or why they would say he wouldn't be going there during his 'normal' routine. If he was looking for missing equipment, for example, he might look in places he might not normally go into if he suspected someone put it there.