Gas water heater turn off the gas valve and water, but leave the thermostat at low level, will this cause some issue?
Assuming everything's in good working order, then no problem. Turning off the gas killed the pilot and stopped the water heater from doing anything by the thermocouple.

However, based on your comments you may have bigger problems than a few wasted dollars from leaving the water heater running. It seems you shut the heat off to the house as well when you left and are worried about the water heater possibly freezing.

The water heater would be the last thing to freeze in being such a big and thick column of water. But yes, it could freeze after all of your other plumbing.

You must winterize properly to avoid damage to everything or just turn things down so they only maintain easier lower temperatures.