Well, I can't imagine what might have been done to the horse, but the footman does say (p. 81) that Miss Kendall had stroked the horse's mane at the beginning of the outing. This seems her only opportunity of tampering with Hecate (and even then, she'd have to be quick!)....unless, of course, something had been done to the horse before Caroline took her out.

Then, there's the possibility that Miss Kendall didn't do the dirty work here.