When I started using faster lenses and focusing manually, I had the same issue -- things that looked in focus in the viewfinder were way off in the actual output. In my case it was a couple of things. First of all, the stock focusing screen is optimized for slower lenses, and doesn't show just how narrow the depth of field is at f/2 or f/1.4. (The DOF you see in the viewfinder is somewhere around f/3.5, in my experience.) I changed for one of the S-type screens from
focusingscreen.com and I love it.
Second problem I had was a mis-aligned focusing screen. Before I changed to the S-type screen, I temporarily shimmed the stock screen with some strips of Post-It note, and this fixed the issue.
I don't know if either of these is affecting you, but that is at least a couple of things to look into.