you will see all kinds of inconsistencies when you zoom into 100%. I suggest not zooming into 100%
regarding the image above, it looks fine to me, but I would not be surprised if the camera focused on a certain area, when you thought it was another. With all the branches and stems all over the place, the camera can get confused.
Maybe try a live view manual focus at 10x magnification and see if the images are in focus and sharp??