It is very difficult to say what should or should not be called for a specific play because there are often other variables involved.
However the basic summary is this:
If you are using your arms to make a play at the disc, and an opponent initiates contact with your arms, then it is a foul by the opponent.
If you are using your arms to block a possible pass, but there is no actual pass at the time, then you cannot call a foul if an opponent initiates contact with your arms. You can keep your arms up when in the cup, but you should take them down if you are aware someone is going to be running past you.