The biggest problem with the PS3 (and Controller on PC) auto run feature is that the directional controls change when you activate it. It switches from camera relative (where pushing left on the control stick moves you left from the direction the camera facing) to steering (where left makes your character turn to the left, independent of whatever your camera is looking at). If you intend to make this change, you can make the mental adjustment to handle the different control style. However, the biggest problem is accidentally engaging auto-run where you're not prepared for the different control style. In this case, your immediate reaction is to pull back on the control stick, which works with the normal control scheme. But with auto-run it now just turns you and sends you off running in some unexpected direction. If auto-run just kept the same, normal camera relative control style instead of switching things up on us, this would be much less of a problem.
TLDR: do not switch control styles when engaging auto-run on a Controller (PS3 or PC).