In a previous thread, I stressed (again) the benefits of manually focusing. Nature being as chaotic as it is, often there is just too many things in the viewfinder that Auto Focus can get hung up on.
I also mentioned focusing into the subject from both the front and rear. This is because when the subject is small in the viewfinder and not in the center, critical focus is tough to see (especially in a darkened environment) and it is not readily apparent exactly when the target "popped" into focus. Focusing from both sides (if there is enough time to accomplish) maximizes the possibility that you got the critical focus exactly right.
Here is a personal example from this morning. These three are from 4 consecutive exposures just seconds apart with a 300mm. First image is a full frame example. You can't move the focus ring with enough precision to correct either rear or front focus problems. You got to shoot what you think is in correct focus, then intentionally move the focus way off, then try again, and again.