Referring to that employee as a skeptic or skeptical might be appropriate. There are a couple of caveats, though.
1) The original meaning of skeptic referred to a school of thought that questioned whether real knowledge was even possible. The scenario given in the question doesn't really go that far, but if the employee has a long history of asking for further analysis of plans drawn up by managers, the word might fit with one of its more contemporary interpretations.
2) Speaking of modern interpretations, the word skeptic has taken on a new shade of meaning. There is a certain brand of "skeptic" these days that denies, rather than questions, the existence of certain things. I'll avoid getting into any of that, but suffice it to say that the word has taken on a bit of a negative connotation.
Note also that the employee in the question isn't really questioning the authority of the boss, but is instead questioning the nature of the plan and the viability of other plans. The fact that it's the boss' plan seems secondary. If the employee was questioning the boss' authority, that might be something else. I might say that employee was undercutting, undermining, or maybe even back-biting.