If you're using Mongoose, you've changed your indexes, and you're wondering why you've run out of RAM, go into the Mongo shell and manually drop any indexes you are no longer using. Mongoose has no method for deleting indexes you're not using any more, so they accumulate, gobbling up RAM.
Now that you've cleaned out those unused indexes, restart Mongo. After the cache warms up (and depending on how many indexes you deleted), you could see a dramatic decrease in RAM consumption.