Now, let's say someone tells you that they're not feeling well or that they're going through a tough time. If you suspect that this person might be lying - saying that they're not feeling well when they actually feel fine, or saying that they feel worse than they actually feel - then it's fine to question the legitimacy. People lie sometimes, and it is possible that someone might lie about not feeling well. What I have a problem with is when we believe that the facts are true, we believe that the person actually feels the way they say they do, but we say that their situation is not a legitimate reason for feeling the way they feel, or that the way they feel is not a legitimate reason for acting the way they are acting. That's for them to decide, not us.
A few of the dictionary definitions of legitimate are "conforming to established standards of usage, behavior, etc." and "based on correct or acceptable principles of reasoning," but I don't think either of these things should be up for judgement, and I don't believe in "correct principles of reasoning." Everyone has their own reasoning.
Finally, think about this: a person who is lying wants to be believed. If someone is going to make up an excuse for not being able to do something, they would probably say that they were sick or had to go to a funeral, since these are acceptable excuses in our culture. If someone says they can't function because the walls are yellow or people are typing too loudly, they are probably telling the truth because someone who is lying would come up with a more socially acceptable reason. And keep in mind that some people lie because no one will accept the truth.