If it's happening, it's normal. But just because it's normal doesn't mean it's healthy.
Being in school means there is a curriculum, and pain is the chalk on the blackboard.
The danger lies is pointing at the chalk, saying it's normal for a blackboard to be covered in scrawlings, failing to decipher what they mean, and grudgingly putting up with them (or putting up with them with faux-spiritual 'acceptance').
That way, you stay in the same class forever.
With physical pain from activity, e.g. long-distance running, the pain is usually a sign of doing something wrong: bad form, no stretching, no mobility exercises. Two people can both run seventy miles a week; one is full of aches, the other, not.
It's the same with other activities. Disproportionate, inappropriate, or untimely pain is not inherent in any situation. It's inherent in a particular reaction to the situation.
When I'm balanced, pain arises, along with a hundred other feelings, and then subsides naturally and quickly, like waves collapsing. It's actually barely noticeable. It's there if you look, as is every feeling, but it's like an individual instrument in an orchestra. You don't hear the instrument, because you're listening to the music.
When it's problematical, it's all I hear, and I can't actually hear the music because I'm focused on the instrument.
It's possible to be calm, centred, and poised in any situation. This, in fact, is the natural state. It's just a matter of working through the distortions that block this natural state.
In sport, pathological pain (as opposed to the 'normal', mildly painful sensations arising after a run) is a result of a distortion. It is not part of the natural process of running. It is part of the running curriculum, however.
Emotional pain: the same.