I hear a loud click at times after the toilet has stopped running, it also runs for a few seconds at times. COuld this be caused by air in the lines?

Do you have a fluidmaster fill valve?

do you have a fluidmaster fill valve?

Are there issues with the Fluidmaster Ballcock I'm unaware of?

If there are, what would you recommend?

The fluidmaster 400 is my favorite hands down. I was guessing that when they said it runs for a few seconds that it was a fluidmaster refilling. As you probably already know, the fluidmaster is either on or off, no slowups. The clicking is probably the fluidmaster simply shutting off and the running for a few seconds is either a leaking flapper or a fill tube syphoning.

I hear a loud click at times after the toilet has stopped running, it also runs for a few seconds at times. COuld this be caused by air in the lines?
The click is not immediately after or when the fill stops, that is what surprised me. The flap is seated properly and not worn. What would cause the fill tube to syphon ?

Syphoning it caused by a fill tube below the water level of the tank inside the overflow tube
Have you considered pressure to high and the fluidmaster may be kicking on at higher peaks? What is the pressure of your water system?