I was going from The Shadow Stone to Lost Tongue Overlook to kill the dragon located there.

I must have taken a wrong turn or something, and I was going east looking for the stairs to get up there. I was in some light woods in the middle of the night, when two enemy icons appear. I go towards them, thinking they are wild animals or something, when the two Companions, Farkas and Ria, start attacking me. I try to kill them, but they are essential, so I sprint away.

Has this happened to anybody else?

Don't know if this is the case with you or not, but some of the Companions are tagged as guards and will go aggro on you if have an outstanding bounty. Unless you've done something to tick them off in particular, like inadvertantly hit them with an attack of some kind (shout, AOE spell, arrow that went off course) or maybe attacked another member of their faction (and I don't even know that this would have that effect) then they may be responding to whatever bounty they think you have.

There is also a glitch that can make them and some "upper echelon" law enforcement types, like members of a Jarl's court, think you have a bounty when the guards don't. There might not even be an outstanding bounty in your stats. The problem with the guards not seeing this hidden bounty is that they won't give you the option of paying it off.

The thing with the Companions is I don't know if they only function as "guards" for bounties in Whiterun hold or if it applies for all nine holds because of their status as general mercenaries and do-gooders. But if you are in the Rift, you can try going to Riften and entering Mistveil Keep. If the city guards outside don't want to arrest you when you talk to them, but the housecarl and others in the Keep go aggro on you, you probably have the glitch.

The simplest solution I've found is to commit some small crime in the presence of a guard in the hold where you are having the problem. Make sure you have enough gold to pay it off, and do that when they give you the option. That should clear your entire bounty in the hold, including any glitchy ones that you can't see but that are causing other people to go hostile.

If the problem is not a glitched bounty in Riften, then I guess you can repeat the process in all the holds until you no longer have Companions attacking you. I would try Whiterun after Riften in that case, since that's their base of operations and their guard status may only apply to crimes committed there.