I've created an example that demonstrates this issue here https://gist.github.com/lukebergen/1ddd897a1635f46c732b.
I've tried to pare this down to the bare essentials of the issue that I'm seeing but it's a little convoluted of a situation.
Basically, if I have a function score that I only want to apply if my field is present, so I add an exists filter to the function. This works great except in the use case where all records are filtered out by this existence filter. In which case an error comes back "Unknown field []".
I'm on ElasticSearch 1.3.4.