The first part of "Paul's Case" introduces us to Paul not as the strange character on whose temperament the story is based, but as the young, mischievous student who keeps his teachers on edge. Although he is, indeed, a different class of individual, it would not be fair to classify his behaviors as "abnormal". Here is why.
Cather's description of what the teachers see is more reflective of their pre-disposition against Paul than on any "abnormality" of his. In fact, most of the description that is given is focalized from the perspective of Paul's old-fashioned, and easily-intimidated teachers.
it was scarcely possible to put into words the real cause of the trouble, which lay in a sort of hysterically defiant manner of the boy's; in the contempt which they all knew he felt for them
This means that it is Paul's haughty behavior, his disdain for the teachers, his shameless disregard for them, and the hatred that he felt for school that perhaps prompted him to act even more strangely than he usually would have.
Now, to be fair to the teachers also, Paul did have some quirks and looks that made him different. First, he was very tall and thin, with a narrow chest and eyes that were salient for their large pupils, which made him look as if "he were addicted to belladona".
The quirk that makes him almost look macabre in the eyes of the teachers is the tendency to grin showing his teeth in an effeminate manner.
...his pale lips parted over his white teeth. (His lips were continually twitching, and he had a habit of raising his eyebrows that was contemptuous and irritating to the last degree.)
That was, perhaps, the most aggravating factor of his behavior.
The proper way, however, to label Paul's behavior should not be as "abnormal". This is because there is not a single exact group of social indicators that, combined, would quantify the meaning of the word "normal". A number of variables play a role in the behavior of individuals. Paul's behavior is a result of his unique temperament and sensitivities; he also obviously lacks anchoring and, to make it worse, he is totally disconnected from his reality. Like the red flower at the end of the story, Paul buried himself in the snow of winter by killing himself after having seen what the beautiful life is like, rather than by letting life show him any more ugly realities.