First off, I have to ask you to define "running". Many people talk about all the app "running" on their device, when the apps are really just loaded into memory and idle. This is the way the Linux kernel manages RAM, to leave frequently used data in memory, rather than dumping and reloading it frequently. It's a big change for people who are used to Windows, but it's completely normal.
As to why you have 3, I'm not sure. It's possible that whatever tool you are using to view the 3 instances it reporting different sub-processes running under Play Services as being 3 separate copies of Play Services.
Do all 3 come back after you reboot? If so, then please elaborate on where you are seeing 3 instances of Play Services running.