Is your socket.io connection on xhr by any chance?
That message is from the system that prevents too many emits, it means the client side made more than 20 socket.emit() calls in less than 1 second. There might be a bug on the client side that is making too many emits.
Open up your developer console(f12 in chrome) and checkout the network tab. If you see a lot of polling requests by socket.io it means it is using polling. I am not sure if that is the cause yet though.