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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.

OP - We are taught to be obedient to our shepherds, the pope, our local diocese bishop, the pastor of the church we attend in our diocese. But yet, few here on CI are obedient to our customary shepherds. We are not obedient because we do not recognize their voice as the voice of the Good Shepherd, the voice of Our Lord Jesus Christ who said:  " He that entereth not by the door into the sheepfold, but climbeth up another way, the same is a thief and a robber... they follow not, but fly from him, because they know not the voice of strangers."  If we do not recognize the voice of the visible hierarchy what voice do we follow? This is the most important decision to make today, for if we blindly follow one of the priests that is going to Hell, we will go there with him. What priest do we follow, THAT is the question!