What you are looking at when you look at almost all leather upholstery is paint.
The leather is basically the carrier for the paint or top coat. The leather upholstery is a split layer of the hide and it is painted and textured with a urethane coating to look like expensive top leather. The leather underneath this top coat is UGLY. When you use the wrong cleaning agent or a harsh abrasive you are risking damage to that thin urethane coating. In this case the texture was not affected but the paint was stained.
Always test the product you plan to use in an inconspicuous area to see what the result will be before using it in highly visible areas. This is important as repair of the secondary damage may cost more to repair than the original damage.
For ink stain repair I'd suggest a product designed to remove ink from leather like this:
http://www.leatherworldtech.com/Prod...r__LMIK08.aspx
Take care to be sure you are only removing the ink stain and not the leather dye.
For repair of the damage now I'd suggest this:
http://www.leatherworldtech.com/Prod...ant__D245.aspx
To prevent ink and similar stains from penetrating the top coat of your leather I'd strongly recommend using this at least quarterly:
http://www.leatherworldtech.com/Prod...__LMPC250.aspx
Sometimes it is best to take your problems to a professional. Often it results in a better, faster repair, and can be cheaper in the long run.
Rule #1... Don't make the damage worse.
I used to have an uncle who loved to play tv repair guy. He would always visit my MIL and go behind her TV and start tweaking things and the tv always looked much worse when he finished. My MIL would occasionally have to get a pro back after he left to correct his wonking around. The pro finally just put some nail polish on the controls so they could not easily be moved. LOL
If you are not sure of what you are doing seek out an experienced pro.