What does STEM cover? Does it include MBA graduates? Does it include HR graduates?

NOC code doesn't depend on education or title of your job but on your role and responsibilities. That's true for Express Entry.

How about those candidates who have strong French proficiency CLB9 and CLB7 in English but overall CRS low due to age factor.

STEM stands for science, technology, engineering, maths. So no, jobs related to mba and HR don't fall under that.