To be accurate the time is not set from GPS. Turning on the GPS uses a lot of power. All that is happening is that some phones when converting times into the local timezone are not accounting for leap seconds. (The number of seconds since Jan 1, 1970 or the 1982 epoch of GPS is unchanged - it is just our human foibles with timezones and arbitrary rule calculations that are messed up.) And only for some phones.

My iPod Touch and Android Phone (HTC) have exactly the same (local) time and both are set to automatic.