Help Required
 

Hi all, i am new to the scene of mechanic on a bike i have just taken off my rear wheel which is quick release and have taken out the quick release and re greased as well as backed of the not holding the gears on so i could get a twig out, reassembled all tightened the nut for the gears and when i but it back on everything lines up, but the nut on the side opposite to the gears is rubbing up against the frame and is shaving off metal when quick release is still loose and with it tight there is no movement at all. Not sure if this matters but i took apart the rear disk brake assembly cleaned off brake dust with air and put back on.

Thanks in advance
Att

It would have been much easier to help if you'd looked up the proper names for the parts first. "Nut holding the gears" = cassette lockring? Locknut for the driveside cone?
Cassette lockring, you'd need a chain whip and a splined tool to touch that.
And DON'T mess with the locknut on a cup&cone hub unless you have a cone wrench and knows how to do bearing adjustment.

And the wheel moving about when the q/r isn't closed is really a no-brainer. You weren't planning to ride it like that anyhow, were you?
As long as the wheel stays put and aligned with the q/r closed, all is well.

Head over to the sites suggested in the posts always at the top of tis forum section, sheldonbrown.com and the Park Tool repair site. Learn the names.
It's also a good idea to use a headline that holds some information about WHAT it is you are looking for help with.

Ok thanks so to fix this grinding problem should i just send it in to my bike store or just get a new group set for the gears such as a shifter, gears, derailleurs all for front and rear as well as new brake triggers, and if i do what is a decent quality mb group set for a good price or is there just a specific part i have to replace

Wow, that's like asking if you should get a new transmission for your car if it's shifting rough, without checking the fluid level. If you don't have a bike co-op nearby I would strongly recommend taking the bike to a shop.

Help Required
 

If you hold the axle ends and wiggle them, do you detect a bit of a wobble? It sounds to me like you have mis-adjusted the cone nuts against the wheel bearings. Doing so would place then other nuts further apart, resulting in the scraping that you notice.

Take the bike to a shop. No real damage is done if my surmise is correct. The problem is common, and is easy for a shop to put right again. They will charge, of course. But they have the tools and the expertise.

Maybe you can post some pictures to better explain the problem.

Thanks dude this stopped me going insane trying to figure out what i need i will bring it in this week and see what they say unless u have any tips for doing it myself and the only visable damage is about 1-2 mm of the bracket for the q/r