One reason could be that Hermione is under a lot of stress in the fanfic, and she takes it out on Sirius. Also, she might have some misinformation about Sirius that makes her think less of him. For example, if there are rumors going around about Sirius' past actions, Hermione might believe them without really getting to know him better. Another possibility is that Hermione is trying to assert her authority in a situation where she feels it's being challenged, and Sirius just happens to be in her way.
It could be that Hermione has a different set of values in the fanfiction. If Sirius' actions or beliefs don't align with hers, she may be condescending towards him. For instance, if Sirius is more laid - back about following rules and Hermione is a stickler for them, she could view him as irresponsible and act condescendingly. Also, personal insecurities on Hermione's part might play a role. If she feels threatened by Sirius in some way, like his popularity or charisma, she might use condescension as a defense mechanism.