Mother Malkin shows cleavage in various scenes, as does Lizzie, and occasionally Alice. The amounts of said cleavage vary, with Lizzie sometimes showing a fair amount and Alice only a little bit.
After Tom rescues Alice from some angry townsfolk, she somewhat suggestively asks what he's going to do with her.
At night, Tom discovers Alice swimming in a pond of sorts, and she is presumably nude, but we see nothing but bare shoulders and her head. She tells him to turn around as she gets out, and we then briefly see her in wet attire, but nothing explicit. Moments later, they nearly kiss, but don't.
Tom suddenly kisses Alice, and she then kisses him back. We later see them cuddled together under the covers, with him seemingly fully clothed, and her with her top off one shoulder. It's unclear, but somewhat suggested that they have slept together, and they kiss again in that position while lying down.
Alice kisses Tom. Tom kisses Alice.