It's a BRILLIANT film, and who did it is OBVIOUS if you pay attention...
SPOILER
It’s obvious either him or his wife did it.
Makes a lot of sense if he knew or at least suspected it (in the film it’s heavily implied he suspected it since he doesn’t really look THAT surprised, but rather saddened that his fear came true). If you watch the movie CAREFULLY it’s all there really pointing to the wife and to him realizing it:
She never ONCE doubts his innocence, to the point of him even asking her about it. Kinda odd for a cheated wife to be 100% sure his obsessed hubbie didn’t do that with semen and fingerprints and fiber pointing straight at him.
The first time we see them having sex is AFTER the news of Caroline being killed. I mean, she’s in almost celebrating mood.
She’s NOT surprised nor shocked about her death.
She only freaks out when his hubbie is accused. She never wonders whether he may be in danger (what if the attacker wants revenge on him also for whatever case he worked alongside Caroline, which was one of the theories they were investigating).
She had clear motive
So it’s clearly telling due to her reactions what really happened.
Now, as to Rusty suspecting/knowing she did it:
Caroline was bludgened to death, which screams personal grievance (as opposed to a say foiled robbery attempt or murder for hire).
The attacker was let inside, so it was someone she knew.
If he’s innocent, how could possibly have his semen be found there? And a glass we later realize came from HIS kitchen set (he MUST have recognized it at some point) with his prints. No matter how badly Molto and Nico would want to frame him for whatever, there’s simply no way they could get his semen. Maybe one of his glasses, but his semen?
The evidence at trial showing that semen actually came from a diafragm (not that somebody just jerked off and placed his goo in her to match Rusty’s A antibodies) that Caroline had no reason whatsoever to use, and that Rusty knows she never wore with him. Unlike his wife. I’m sure at 49 years old he knows if/when his wife wears a diafragm.
See? It all adds up eventually. So he MUST have suspected her at the end. His clear lack of reaction at discovering the bloddy axe proves it.
Now why frame her hubby if she didn’t intent him to be charged?
Clearly she’s not a career criminal, so she was stupid enough to think such a move would not have severe consequences regardless of who was in charge of the investigation (like people say, any cop stumbling into that would suspect Rusty).
Maybe she on a subconscious level wanted to hurt him, as payback for the affair.
She is already disturbed due to the affair, as her behaviour suggests in the movie and the way she confesses at the end, so no wonder she did such a thing.
And if anyone wonders why would Rusty cover her crime, isn’t it obvious?
He’s feeling guilty as sin for he considers responsible for all of it (his affair set off this chain of events). So if anyone should suffer for his wife’s crime it should be him.
He feels he owes it to her since she forgave him for the affair. Which makes total sense since it’s common knowledge that Caroline was an opportunistic slut who targeted whomever she felt could advance her carreer. Since everybody knows she targeted Rusty (even local cops state they knew she was inquiring about him before they ever met), clearly his wife knows it too, and since Rusty is not a womanizer as stated in the film (it really was THAT one time), it’s a lot easier for a wife to forgive knowing she needs not to worry about a repeat.