According to the 1839 edition) of Robert Southey's _The Story of the Three Bears_ it was because their chairs' cushions were disturbed:
> "Somebody in my chair has sat!"
> With voice so gruff and great
> The Huge bear said, when he saw that
> His cushion was not straight.
>
> "Somebody in my chair has been!"
> The middle Bear exclaim'd;
> Seeing the cushion dinted in
> By what may not be named.
The wording was slightly different in the first edition (of 1837). The history of this story (and its publication history) is interesting and complex: see the Wikipedia article on it. In particular, the identity of the home invader has changed.