Some time ago I was in whiterun and I was heading for Jorrvaskr. I was in the back area when all of the sudden Athis and Torvar starts attacking me. I decided to have some fun so I decided to run all over whiterun casting spells (to help increase my levels) at them. Eventually I got bored of it and thus I started getting serious. Both were easy to defeat and I wand up killing both of them. Their bodies went idling at the same spot for sometime (approx a week or two or even more in Skyrim time) until I came near Torvar's body again. A guard came up to me and started interrogating me right before he grab something from the the body. I remember not having any bounties over my head in whiterun after killing the 2 men, since they provoked the fight first. The guard eventually threw me right in the Dragonsreach Dungeon for a few days.

I started thinking and I remember a similar thieves guild job that was given to me by Vex, http://www.uesp.net/wiki/Skyrim:The_Shill_Job. It it possible that someone that doesn't like me in whiterun hired the thieves guild toss me in prison?

You probably did something wrong like casting a random spell or something.

I'm not sure about it, but you might have been detected when planting the evidence during the Shill Job, maybe adding bounty, causing Torvar and Athis to attack you. People sometimes become hostile when you are caught committing a crime.