I think it is most likely an inconsistency, the point taking by Percy seems to have been a one off incident. In Order of the Phoenix, Ernie said that prefects can NOT in fact take points. I think it is to draw attention to how unjust and unnatural Umbridge's order is.
Ernie is right, Malfoy being able to remove points is ridiculous! 😂
"Oh yes, I forgot, you're a mudblood Granger, so ten off for that!" Hermione cannot do anything right as she is a rule breaker by her very category according to Malfoy's rule! Just imagine if he had been able to take points off for a whole year!