I'm using an audio control LC6i in my ford fusion that has had the "thump"/speaker pop issue on shut off since I installed it. Typically I think the LOC(if one is being used) is the culprit here. I'm using its GTO feature to turn the LOC on which turns the system on which is where my problem comes from. If memory serves what causes it would be the head unit turning off before the amp. I didn't have much luck fixing it so I decided to live with it. If you are having a similar issue, you could try wiring in a physical shut off switch to the REM wire on your amp then try shutting it off first before you turn the car/head unit off and see if the issue still persists. From there I'm not sure what to do since, like I said, I could not figure out how to fix this issue myself.
Knowing your full setup, such as factory or after market head unit, LOC(if there is one) and such would help as well.