Madoka had once asked Homura to try to get along with Sayaka. It had been an innocent request, made in the spur of the moment as the two other girls had been shooting glares at each other for some childish reason or another, but it was one that Homura remembered to this day all the same. She would never forget something Madoka asked of her, after all.
Yet at the same time, it was also the one thing Homura knew she could never do for Madoka, no matter how much she tried - not that she ever really had, or would, but that was part of the problem.
Sayaka was a fool. She was a fool in love with a fool that would never listen to her, no matter how much she wanted them to. She was a fool who would give up everything for a fool who would never look her way. She was a fool who put her feelings above the feelings of everyone else, despite the destruction that her actions and feelings brought to the world around her. She was a fool who let her feelings be so easily manipulated by another - she was chained to that, and no matter how many timelines Homura visited, she knew Sayaka would never escape her fate.
Why did Homura know this?
It wasn't because she had seen it happen so many times.
It was because Homura herself was a fool. She was a fool in love with a girl who always, without doubt, made that contract no matter how many times Homura told her not to. It was because Homura was a fool who had given up everything for a girl who always looked out for everyone, a girl would never remember the reason Homura had given up everything for her in the first place. It was because Homura was a fool who had put the safety of one girl above everyone else, not caring how many times she watched the world and people she should care about go to hell in the process of searching for the one world where that one girl she cared about so much remained safe. It was because Homura was a fool who had oh so willingly let herself become entranced by another, let her world revolve around them - she had become chained to that pink haired girl, and no matter how many timelines Homura visited, she knew that in the end, all roads would lead back to Madoka.
The reason Homura couldn't make nice with Sayaka was so much simpler and yet so much more complex than "she had seen Sayaka cause problems before so she had decided Sayaka wasn't worth it" or anything like that.
The reason Homura could never accept Sayaka was because it would mean accepting the monster that Homura herself had become.
And that was something Homura could never do.