Absolutely, I've had it happen in "big" (client-side) JS projects.
Only way I've found so far to handle this is to make anything which might ever have any reason to become asynchronous (so anything but helper functions) take callbacks or return deferred objects. Always.
But then an other issue arises: for various reasons, callbacks-based code which works synchronously may fail asynchronously, and the other way around. And then it starts getting real fun as you still have to go through all your (supposedly) carefully constructed callbacks-based code to find out what reason it would have to fail (alternatively, you create both sync and async tests for all pieces of callbacks-based code)