Gina, I'm new to this forum but hope to learn a lot about the Focus Electric from the people here. Living and working in the auto industry in SE Michigan, and knowing several of the Ford engineers on the program as well as some of their suppliers, I've learned a fair amount about the "inner workings" of the Focus Electric. However I'm not professing to be an expert.
One thing I do know about the Focus is that the battery cooling system may potentially run any time the charge cord is connected. As long as the vehicle is plugged in (whether its charging or not), the thermal system will monitor the battery temperature. So even after charging is complete, the cooling pumps (there are three of them) and AC compressor can come on and off to keep the battery at the desired temperature. If the air temperature is very high where your vehicle is parked (such as in a closed garage) while on the charge cord, the pump(s) and compressor will come on and off to keep the battery at its required temperature even if it has stopped charging. This may be what you're hearing. The pumps and compressor are all located beneath the hood.
Also, in cold temperatures with the vehicle plugged in, the pumps may run (and the coolant system heaters turned on) to warm up the coolant. So may may hear the pump(s) run in cold weather too if it's plugged in.
You may very well be experiencing a normal condition. However if you feel there truly may be an issue, obviously it's time to bring your Focus in to your dealer so they can check it out for you and give you peace of mind.