> var start = new Date()
> var c = db.test.find({$where: function() { sleep(10000); return true; }});
> c.maxTimeMS(1000)
error: { "$err" : "JavaScript execution terminated", "code" : 16712 }
> var end = new Date() - start
> end
10021

Set the sleep to 10 seconds, set the timeout to 1 second. Run a timer, it only terminates after the 10 seconds are up and not the 1 second...

Since javascript $where doesn't allow yielding, or checking for the kill signal for that operation, it runs through to the end of the execution.

The same thing can happen with a page fault or other long running part of a query/operation.