With the 60D's 9 AF points, auto selection wasn't terrible - if it picked the wrong subject, you knew. But with the high density 61-pt array, you can get a lot of shots that are just a little off, it'll grab the shirt instead of the eyes, leading to OOF shots. Combine that with the thinner DoF you get with the same aperture on FF vs. APS-C, and you've got even more slight misses.
Spend time with the AF system. In Custom Controls you can set the multicontroller so it directly selects AF points. You can specify a default point, even a different default point depending on camera orientation. Pressing in on the multicontroller takes you to the center.