So, you must sift each and every command, even when it comes from certainly lawful authority? That is NOT obedience; that is making oneself the final arbiter of the merit of each and every command.
Yes, you must use your God-given reason and listen to your conscience. This is what St. Thomas Aquinas, and all Catholic theologians, taught.
Regarding a questionable "command" from a human being, you should compare that command to the authentic Magisterium. If the command contradicts the Magisterium, you must reject the command. Otherwise, anyone one in any religious order would be subject to the dictatorial whim of a superior. The words I quoted above from St. Thomas Aquinas show the proper method for "sifting" these commands.