Do you trust your own instinct?
Have you ever tried to sell something to someone and thought that although they said the right things, this sale will backfire?
Have you ever met someone who seems OK but something is nagging you about their behaviour?
Have you ever gone along to a meeting and it has not turned out as you expected?
Don't worry, these are all examples of you trying to make sense of the world.
Your instinct is a very powerful tool. It is a whole host of memories and analyses dragged up from the depths of your brain and based on the amount of time you have spent on this planet.
You may not be able to instantly recognise the problem, but your feeling of discomfort is driven by your subconscious mind telling you this is not right.
Learn to trust your instincts and don't be persuaded otherwise. You may of course not be 'right', but most of the time you will be, as the definition of 'right' is purely your personal definition and hence driven by your instinct.
I would suggest there are some parts of your instinct that need curbing (that desire to throttle someone who is annoying you), but most of the time your instinct is trying to help you make sense of the world.