How do I adjust apple crisp cooking time for muffin-size crisps?
According to the book Kitchen Companion, when you take a square cake and cook it as cupcakes, you cut the baking time by 40-60%, depending on the relative depths of the two pans.  I'd assume the relative cooking time for a crumble to be similar, which would mean 25-35 minutes.

There are also a number of apple crisp/crumble recipes on the web done in muffin cups or small ramekins, and their cooking times range from 14 minutes, to 25 minutes, to 35 minutes.  The 35 minute ones sound the most similar to what you're doing, so I'd say start checking them at 20 minutes, but expect 30ish.