It's probably because some of the rubber bushing are destroyed that keep the engine from shaking when you hit bumps and when it starts and stop. Check the motor mounts first.  

Hello,

This sounds like a case of "running on"

When the engine is turned off it continues running with knocking and rattling sounds.

The problem can cause problems as sometimes the engine can runs backwards,

Some of the causes of running on are, Overheating, Incorrect ignition timing, Cheap Fuel,Carbon build up.

You should really have this looked at by a Mechanic

All the Best.

Is it coming from near the engine or inside the engine? 

If you mean near the engine, check your engine mounts. If it’s coming from inside your engine, look at the answer above.

Either way, get it checked by an honest mechanic.