There are typically a couple/few reasons this can happen:
1- Pulley teeth are worn down and no longer hold chain in line
2- Pulley isn't installed correctly.
3- Chain is too long, and "droops" off pulley
4- Derailleur hanger is way out of alignment
5- Derailleur cage is bent


Those pictures aren't really good enough to say for sure, but it looks like your derailleur is out of plane, which would be 4 and/or 5 on that list. Even with this being the case, you typically need a bit of 1 and/or 2 to see rubbing like that.

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Looks like your rear derailleur hanger is bent... Theres a piece called a derailleur hanger that is made to bend and protect your derauiller and frame. You can buy a new one for like $10 or get a tool that fixes them for $60.

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Strava

I'd also guess 4 or 5. Leaning toward 4 (bent hanger) based on the pics (the hanger seems bent in relative to the QR nut...but that could just be the photo angle). Some square shots from behind the bike would help, including a closeup of the rear dropout and hanger from directly behind.

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ECMGN Therapy Silicon Valley:
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Hi there man!

I will change the hanger but, I really feel like the problem is a worn out pulley wheel. Makes the most sense out of what you explained.

Thank you!

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it looks to me like the RD isn't installed properly, there's a big gap between the RD and the hanger. if it's cross threaded then that's could cause that.

I don't think its a worn pulley. that shouldn't affect the angle of the RD cage itself, which it looks to me like that's what the issue is.

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Hi Jason, You mean I accidentally cross threaded the hanger? I'm looking at it closely now. Hard to figure out what went wrong.

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Odds are you've got more than one thing going on here, and they're "complementary" parts of the problem. Even with a cross threaded/bent/out of alignment derailleur, it's pretty rare for the chain to hit the inside of the cage if the pulley wheel is in good shape.

Better pictures would help a lot. Take one from the side, take one from directly in back. Don't take them from an angle, that makes it really difficult to tell what is parallax error/lens distortion and what is physical alignment.

You can check for cross threading of the derailleur by simply taking the derailleur off, then re-installing. If it threads in at an angle and doesn't seat flush at full insertion, the threading is off.

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Tech writer/support on this here site. FIST school instructor and certified bike fitter. Formerly at Diamondback Bikes, LeMond Fitness, FSA, TiCycles, etc.
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Is the end of B-Limit screw sitting flush on the shelf on the hanger?
It looks like it might be against the side (ie. the threads of the b-limit are touching the side of the hanger shelf), which could be causing the derailleur to not be fully screwed in / misalignment.

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Derailleur hangar may not be in alignment. Invest in the Abbey Derailleur Hangar Tool (i know it's pricey, but it's worth it). Start there. Then see what other problems may arise after that.
For full disclosure, I bout the Abbey derailleur tool, and I use it on all my bikes anytime I make adjustments. For my race bike, it was a game-changer by showing that the derailleur angle was way off.

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Best pictures I could take.

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http://www.easyendurance.wordpress.com

There shouldn't be a gap where the RD screws into the hanger. I just checked mine, I have the exact same RD (Dura Ace 9spd). If you've been riding with it like that for a while, it may have eff'd up (thats a technical term) the threads on the hanger.

this is what it should look like.

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How do you post pictures that can be enlarged?

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I upload to imgur.com and put the link in - the one with [img tags.

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Hanger looks like it might be bent of twisted. I'd recommend the following:

0.5. If you have an old RD, you can mount that and see if the cage is || to the cassette (if it is the problem is the other RD, if not it's probably the dropout).

1. Remove the dropout/rd hanger and place it on a flat surface to see if it's bent/twisted (if so, replace).

1a. If you have a spare frame you can mount the RD and see if the cage is || to the cassette on a wheel you insert. If not the RD is damaged.

2. If it's ok, reinstall it and remount the RD making sure it mounts flush.

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ECMGN Therapy Silicon Valley:
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The other trick to checking the hanger straightness, assuming you don't have access to a hanger alignment tool, is to grab a second rear wheel off another bike (as long as it has a threaded axle) and screw it in to the hanger (after unscrewing the derailleur of course).
The two rear rims should be parallel - measure the distance between them at various points around the circle. (Rotate both together and measure at the same point, e.g. the valve hole, for consistency)

I use the front wheel

How? it has a different thread size. (9mm vs 10mm)

If the threads on the hanger are trashed you can clean them up with a tap and some oil, it's soft metal. The Rd just needs to be screwed all the way in.

Also, if you happened to have removed the jockey pulleys make sure they are in right, there is a top and bottom

Finally a problem I know the answer to! You forgot the cassette.

shit. I was wondering why I was so slow, thanks!!

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