I think that the possible number of "bad" decisions outnumber the possible "good" decisions. If one is randomly selected, it's just more likely to be a "bad" one.
I'm going with this one. To use the "dwarf running from an enemy" situation as a basic example - there's probably one, and exactly one, "path to safety" that will get the dwarf to your trap-laden entrance and shred the enemy (after all, if you went around scattering dozens of entrances to your fort across the map, it'd be hard to keep the fort secure. Unless you then routed these scattered secondary entrances all to a well defended underground main entrance.. hmm.). But anyway, there's probably one path to safety, and on the other hand dozens of ways to run that do
not lead to safety, resulting in a messy death. Dwarves aren't deliberately being stupid (i.e. avoiding the "path to safety"), they're just not smart enough to recognize that one correct choice, so they make a somewhat random choice based on the happenstance positioning of the enemy and other obstacles, and the availability of many poor choices vs. one good one means it's a rare dwarf who stumbles across the one right choice by luck.
It applies to many other decisions if you think about it - there's only one good choice you want your mechanic to make, hook up the lever to the drawbridge before the goblins get here, and plenty of less-than-optimal things he could do instead (eat, drink, sleep, make more mechanisms, collect sock..), so the odds are just against getting what you want. Or you want the hauler to get that miasma-spewing corpse out of your trade depot, but there are hundreds of other things he can haul instead. It's possible for the experienced player to tip the odds a little in your favor by eliminating bad choices - forbidding the sock and suspending the mechanic's workshop, or setting at least one hauler to only do refuse/burial - but in the end it's a complicated game full of less-than-optimal choices for your dwarves to make, and you just can't prevent all these bad choices.
I think if you pay close attention to the very few situations where there's only one bad choice to balance out the good one - like the classic example of walling off an area, usually there are only two sides of the wall to stand on - then you'll find it generally does come out to 50/50, the bad decisions are just more noticeable/memorable. In fact, for very simple decisions like this, it's possible to gain some insight into how the dwarf makes the decision (i.e. mason prefers to stand north of the wall) and even bias things to have a more-likely-than-not shot at getting the good choice. But simple decisions like this are the exception - DF's complexity ensures that most dwarven decisions are far beyond any easy understanding of how they're made, and bad (or, at least, less-than-optimal) choices far outweigh the good one(s).
..That being said, it's a hell of a lot more entertaining to let yourself believe that they're being deliberately contrary to your fortress's success and their own well being. It's not very dwarfy, after all, to do things the
easy way..