I just read on a similar post the other day (poster had issues with her 50mm 1.4) that some focusing issues may have to do with "focus shift". Below is the link to the thread I read and also the link to an article on focus shift that was provided.
This totally helped me because, like you, I too was having some focus issues with my 50mm 1.8. I thought I was focusing on the eyes, but then the shot turned out with the mouth in focus. Errrr. But the focus shift issue explains it all to me! So, HTH!
Need serious help with my new lens!
http://diglloyd.com/diglloyd/free/FocusShift/index.html
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Nikon D200 & D40, 18-55mm, 55-200mm VR, 50mm f1.8D, SB-600 Speedlight
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