Logan could murder Lily, and then turning him in! was that there was much more solid evidence that Duncan was the one to blame. After all, why would the Kanes be covering up the crime if they didn't have some reason to think Duncan could have done it? And she knows that Duncan had a disease that could make him flip out and kill someone.
Yet she sat on the evidence that proved that Lily wasn't killed at the time she was, that therefore erased all of the Kane's alibis, and proved that the Kane's had to have actively conspired to change the time of Lily's death to protect one of them. Plus she knew the Kane's paid off someone to confess to the crime.
All of that because again, they had to have been thinking they were protecting one of their own. And as good a friend as Logan was to Duncan, they wouldn't have done that for him.
And sure, Logan could be a jackass to Veronica, though hitting someone's car after you get them arrested and suspended, and goddess only knows what his father was going to do to him for that --Logan sure didn't --so can see why he'd be a bit pissy. Is a bit different than being able to kill someone you love. And speaking of, while Logan was a jackass, Duncan sat by and let it happen. He never tried to help Veronica. Never told his friends to back off of her. The way that Logan was willing to do at his party after just being with her for a few weeks.
Duncan didn't deserve her trust either, and to me proved he shouldn't be trusted. And again, had to have been somehow involved...and yet she didn't turn him in the second she found evidence. Nope. That she wanted to prove first, make sure about.
But then the whole forgiveness for Duncan vs. Logan thing is a HUGE problem I had with Veronica. It was bad enough in S1, but S2 makes me stabby. It was one of the things that made me stop liking Veronica as much as I did from S1. That and the smugness.