You did the right thing, Having the wind in your favor is my single most important thing I worry about when stalking deer. Their noses are phenomenal.
Yes a rutted up muley will stink to high heavens. When you harvest one, you will know what I am talking about. They have a very noticeable, musky smell to them.
Whether or not you did anything wrong or not, I would say, the only way you learn is to make mistakes. Sometimes, there is just nothing you can do, and other times you realize you made a crucial mistake during your stalk. Sometimes it is better to wait them out and hope they go your way, other times it is best to stalk right in on top of them. Keep the wind in your favor and judge each deer individually . There is no right or wrong answer as to whether to wait, or stalk in. Each situation dictates your action. Keep at it, and soon you will be successful.