I corrected some of my flagrant misfingering of the bottom row (c with index, m with middle finger, etc) when I switched to Colemak and learned for the first time what the standard fingering was, but I have retained my old barbarian ways for the punctuation characters.
I tend to use the ring finger rather than the prescribed pinky for many of the punctuation characters and backspace. I use the right pinky only for Enter and backslash. In addition, I type left-paren with the right index, and right-paren with the right middle finger. I use parens a lot as I use Lisp fairly frequently, so I've unconsciously dedicated my strongest fingers to them and can sense them pretty easily if non-standardly.
I don't use right-shift. I thought it was just bad habit, but I was surprised and heartened to discover a valid justification for avoiding right-shift: it is measurably farther away from the center of the keyboard than left-shift is. When upcasing q, a, z, letters that normally require the left pinky, I hit left-shift with the pinky and the character itself with the ring finger. I've never found this confusing, although it seems like I should.
I try to type the numbers with standard fingering, but since typos are unacceptable here, I slow down considerably, sometimes to the extent of using the right index for everything when the document is very important. In typing tests, numbers are my downfall.
All my "incorrect" keyings were learned without any intent to do so, and now it's too late or too painful to unlearn.