I was working on the Dark Brotherhood questline and I think I may have activated the
the Companions quest bug in a very new way. Without hitting the two local places that are
used in the companions quest I visited Whiterun and went and messed around at the skyforge to
play with smithing skills. Instant Vilkas in my face and he won't leave. He even followed me into my house.
He followes me EVERY WHERE. This of course triggers the guards following you bug so you can't fast travel.

So then I said ok FINE maybe just doing the Companions quest line will make everything better. WRONG. Now he
talks non stop and I can't even fight during the quest. I do have plenty of saves so going back won't be to much of
a problem. I'm just wondering how far back I'm going to have to go.

From what I have been able to gather via google this is a MAJOR bug and any work on anything else should stop until it is fixed.

Why does everyone think this is a bug?

When they get in your face they're telling you that you have a bounty. Some of the Companions are set as guards, except they can't arrest you. Figure out where your bounty is and take care of it, then he'll leave you alone.

One problem I and others have paid the bounty on coming up on Whiterun, before even entering the gate guards nab you and your dragged to the castle to pay the fine, the bug still happens.
This is how I recall it happeing. I came to Whiterun and much to my surprise there was a bounty so I paid it. Then went to my house and did a inventory swap out. Then went to the skyforge and
well the rest is in my original post.

You're absolutely 100% positive you have no bounty anywhere else? The Companions will still haunt you even if it's not in Whiterun.

When doing the Dark Brotherhood quests, quite often you can pick up bounties without being aware of them. You'll probably find you do have a bounty somewhere in one of the other holds. As others have said, this is not a bug with Vilkas & farkas, but a result of them being tagged as guards, but without the guard dialogue. Once you have cleared all bounties, they'll stop harassing you. Alternatively this can be fixed by setting the Companions to accept all crime through the CK, or finding a mod where it has been done for you.