weird sound after shutting off engine
 

i bought a 2006 RX8 6 spd MT lyk 3 weeks ago and well it was my first time driving stick. i stalled the car a lot but now im driving perfectly without any trouble. just recently i been hearing a weird noise after turning the car off. when i shut the engine off i hear almost like a click, sounds almost like a short grinding noise coming from the engine. i tried leaving the car in gear because i usually shut off the car on neutral so i thought that would help but it still didn't solve the issue. Any ideas why?

I don't know why, but I have an auto and it happened before and after I got my engine replaced so not sure if it has something to do with the engine or not.