For checking front/back focus, read this page, print the target and test the lens.
My 2 cents. The first photo (assuming it's about 3 feet distance from lens to focus point on the subject) you have 3.3 inches DOF. If you didn't focus/recompose, the camera likely focused slightly to the right of the microphone on the boy's chest. This is probably consistent with the few hairs that show sharp behind the right ear. Camera shake could be contributing since this is not an IS lens. In theory you should shoot as a minimum SS=1/(FLx1.6) for a crop, which come to 1/54.
I found that learning to shoot with the back button (BBF) helped me take steadier shots at AI Servo.
The second photo, assuming a distance of 4 feet, has a DOF of 1.5 inches... f1.8 can be soft on the nifty (mine is not that soft...) Keep in mind that if you focus with half pressing in One Shot and then fully pressing once you locked the shot, if you move half an inch in between, everything is going to be OOF. Regardles of the subjects being still and your shutter shooting at 1/1000.
Take the recommendation and test
a) Do the lenses front/back focus (done at the proper distances, with tripod and good light).
b) Once you confirm that you do not have a problem, try the same photo with tripod at different apertures, to see the effect of DOF
c) Then try 'freehand' to see whether you can improve your technique.