It could be surveyed from 2 aspects. Firstly, the word "Sect" has not a negative meaning, or at least its meaning is not negative at using about division of Islam groups. Hence it could not be a problem to use such a word. The meaning of denomination and sect relatively are the same, so, as far as I know, the word "denomination" commonly is used for Christians, but the word sect usually is used for Muslims. Thus we can not say that why they use them like this.
For instance, we have a tradition from the Prophet (pbuh) that mentioned:
After me, my nation(ummah) will be divided into 73sects, and solely
one of them will be saved (will go to Jannah).
Accordingly, Prophet Mohammad (pbuh) would not use it if it has a negative connotation. Besides, if occasionally it uses as a negative word (from an sight), then we cannot say that it is absolutely a negative word, can we?
On the other hand, supposedly, if it has not a positive connotation, so it could be related to the issue that most of those sects ( 72 out of 73) are perverse and actually one of them will go to Jannah. As a result the word sect, in the negative case, could be related to the majority not just one.