So I  am new to harleys but I know the motors make noise but I was sure there was something making a noise that wasn't right, so I decided to pull the outer and have a look. I checked right through and there was nothing, no marks on compensator, clutch basket or chain till looked inside the outer cover.

This is the bolt hole at the front just below the compensator and the marks look very much like the chain.

The tensioner should prevent that. But grinding a bit away wont hurt. 

Thats what I  thought and thats why I am asking, all looks normal inside but don't know what to look for.

Mine is a 2011 blackline and it would be the left hole but on the outer cover.

Doesn't make any sense
the chain feeding off the bottom of the compensator sprocket is not going to move that far sideways in that location now matter how loose the adjuster is
you say you are new to harleys and the bike is 2009 touring
my guess is a previous owner has had some problems with it
the compensator bolt may have come loose and allowed the compensator to move out
or something hanging off the side of the chain and flicking the cover as it goes past ?
Doubt it is a problem now since that chain looks ok
if you have a noise look elsewhere
most compensators/clutch/primary chain are a little noisy
check everything for slop (clutch basket too)
button it up and use a screw driver to check for noise at that location and elsewhere
keep an eye (or ear) on it but don't stress too much

could enquire with the previous owner or Dealer and may find an explanation for that

It's pretty obvious it is the primary chain touching the outer.
Some models have the primary chain running partly outside the inner primary.
It is also obvious the outer has been milled for clearance from the factory.
A pic of the  inner primary showing the chain will clear things up.

As I said there was plenty of meat on the cover to grind some off so I took of the marks and a bit more and there was still of the cover left for strength. I don't know if this was the noise I heard but I feel better after looking, I have no idea how the chain could have contacted at this point and everything in the primary looked like new and a thing of engineering beauty. I did start the bike with the cover off for a short time and the chain ran perfectly with flex only along the top long run and none where the marks would have been but there was strain of changing up or down through gears, just have to listen for the odd noises and live with it.