Very well put by Yu Zhang.
I just want to add my two cents to cover another aspect of it.
Even if we think that the manager's suggestion is incorrect. Before reacting, it is always good to spend some time to think about the suggestion and come up with all the benefits and drawbacks of following the instruction. Apart from that we should also discuss our thoughts with friends and colleagues to get their view about the instruction ( which you have rightly done by discussing on this forum).
In case, even if implementing the suggestion won't be fruitful then we need to be careful about the words that we choose to respond to the manager (or be it anyone).
At the end of the day, we need to make sure that everyone is motivated. If our reply demoralizes someone, then that is not good since manager can also make a mistake.
My way: Go for one to one meeting instead of email
My way to deal with such situations is; to have a one to one (in person) discussion with the Manager. I will generally start sharing my thought about the suggestion in a way as if I want to acquire more knowledge about it.
How do I always get positive outcome in such scenarios?
First of all, be courteous when starting such conversation and don't start as if you are going to discuss a very big issue. Just start as if this is another thing that you want to discuss. I have always got a positive outcome in such a conversation. By positive outcome I mean, sometimes my manager put light on the aspects that I was missing and sometimes I talked about some aspects that he had missed. So, either I convinced him or got convinced.
How can such conversation go in wrong direction?
From my experience of last 10-12 years, I feel that such issues are easier to resolve if our intent is to get the perspective of other person or share our perspective. Such issue take a bad shape when the conversation revolves around "who is wrong?". Then start the ego issues and so on.