I think I sometimes try to explain why it's not clear to me (for example, why it could be either of two possibilities) but then it comes across as if I'm asking a question that I already know the answer to. Or even I ask a question and when they answer I ask why the other possibility wouldn't work. On my first day of work a coworker pointed out that it sounded like I was asking questions I know the answer to.
It's hard to say exactly what it is you're asking. Since your title says you want to ask a procedural question, I'm assuming you're asking why certain things are the way it is.
To be truthful, I can totally understand why someone would be annoyed by it for two reasons:
If it is a procedural question involving how to do something, then you can look that up yourself.
There's no rhyme or reason why something is the way it is. Sometimes it is the way it is and of course, it can go the other way, as you say, but debating about it is totally pointless since it is the way it is currently. There's no way someone could change it and on top of that, most people probably don't care. They just do it and continue on with their life.
Sometimes #2 is very obvious to everyone but since they cannot change it, they really don't talk about it or discuss about it. For most people, they worry only about things they can change or have influence on. Since something is done the way it is, they just try to work around whatever it is, even though they know there is a much easier way to do it.
A good example might be, "Bob, do you know how I can submit my vacation time on the time card?" "That sounds like something you can look up yourself in the HR documents, but it is on -insert where it is-" "Oh that's strange, Bob, why couldn't they just do it easier like make a vacation drop down?" "I don't know and I don't really care. Stop asking me."
Instead you should look it up yourself, enter the hours yourself, and do it yourself. Perhaps joke with Bob, "Bob, this time card stinks. The vacation is so freaking hard to enter." "Yeah I know right, they really make it hard for us."