Using manual focus in a situation like this caused you to miss the proper focus area by only a few inches...there just is NOT much depth of field using a 50mm lens at that distance...a 50mm on an APS-C format camera is a short telephoto lens, and at close range, there is NOT much depth of field, even with the lens stopped down to say f/8. I would think that the camera's AF system would have done a better job of focusing. MOST APS-C cameras with small, low-magnification, pentamirror type viewfinder mechanisms are challenging to focus properly in any type of fluid or "fleeting" situation. The viewfinder of many cameras is more of a quick "approximation device" than it is a useful instrument for manual focusing.
Part of the difficulty with modern, d-slr cameras is that the viewfinder screens, on which the aerial image is actually SEEN, are not optimized for focus ascertainment by the human eye; the viewfinder screens are sometimes made artifically BRIGHTER, by a supplementary illumination system (as in Canon's transmissive system), which makes for a really BRIGHT viewfinder image--BUT a viewfinder images that impairs accurate focusing when a human eyeball and brain are used instead of a computer brain that is in total command of an ultra-precise focusing motor. The actual, as-seen-through-the-viewfinder depth of field is often that of about f/4.2 or so, meaning that the SHALLOW depth of field of your 50mm lens's f/1.8 aperture is actually NOT the kind of image your eye sees!!!
Manually focusing an AF lens is also complicated by the really RAPID rate of focus shift the focusing ring of "most" AF lenses have at distances beyond say 3 feet: the lens moves from 3 feet to 7 feet, then BOOM! it is at Infinity within 10 to 15 degrees' worth of turn of the focusing ring...which utterly KILLS the ability to focus precisely when a human is doing the turning and the evaluating.
Simply put, almost ANY Autofocusing normal lens is a bugger to get focused unless all the conditions are perfect. Your SL1 was designed to be used with the camera's autofocus system driving the lens to the exact, right focusing distance.