I've always felt that the Wii Remote's directional pad can be a tad inaccurate when quickly changing what you're pressing. What I mean by this is that, for example, if you quickly slide your finger from left or right to press down, it'l often think you're still holding the previous button for a split second. I've also noticed the occasional inaccurate input which is indeed not caused simply by fat fingering the D-pad. It can seem like the buttons don't always yield what you're pressing on rare occasions in my opinion.
I'm led to believe it's the controllers' design faults overall, sadly. Not something easily fixed, if fixable at all. If a Classic controller can be used to play Dr. Mario perhaps said controllers would be more accurate, though I can imagine buying yet another two controllers would be a rather irksome waste of money... Particularly if the problem still persists even in this different controller.