People saying YES but meaning NO

I've come across this a frequently and I find it very difficult to deal with when people say yes but in fact mean no. Today, my line manager did it again in response to me asking for leave- essentially saying yes in the first sentence but then saying no in the second by saying that he wants the work started this week etc and does not want a delay. This time it was obvious but often when people talk it can be even more confusing to understand what they actually mean. I find this very hard to deal with as it leaves me constantly second guessing what is meant and I just don't understand the point of  this. If it is NO why not just say NO? Why pretend to say yes when you mean NO? Have any of you come across this? Why do people do this? I wish everyone could just clearly say what they mean... it would save so much time, and avoid much anxiety and stress... Why do some people not say what they mean? How can you tell what they actually mean?