1. Intentional Traps: This is less common that it once was, but not gone. Sometimes designers decide they should include bad choices in characters creation/advancement, just to catch the newbs and "reward system mastery." (Looking at you, Monte.)
2. Too many options: This is the same as above, but without the intentionality. there are just lots of options, and not all of them are good, and some explicitly bad, but not because the designers intended it. Maybe they just weren't good at their jobs, or there are so many moving parts it is impossible to know until the game is in the wild.
3. Player unfamiliarity: This is probably the most common result. The player just doesn't know what works and what is good and picks stuff because it sounds like the thing they want to do.
4. Player intentionality: the player knows something is suboptimal or even bad, and picks it anyway -- probably because it fits their intended theme and character fantasy.