To break in means to train a horse (see No. 5 definition in the link).
The sentence could be rephrased to:
Now, it so happened that Maggie owned a horse which was not trained
but was still a bit wild.
When you break in a horse, you don't mean you separate it into pieces as to break literally means. It metaphorically means you interrupt a continuity of its wildness (being wild) and get it domesticated or trained.
Many English idioms and phrases have metaphorical senses and you need to understand them on a case-by-case basis.
Wild is antonym of trained or domesticated.