From what I'm hearing...what happened to you started off as what's called an "interview". Meaning, the first guy was gauging your reactions to see what you'd allow, what he could get away with. This is generally done as a prelude to a robbery or worse. It sounds like they were both drunk or otherwise intoxicated, and the second guy (who was the one creeping you out most, if I'm reading that correctly) may have been more drunk. If I had to guess, I'd say they were at cross purposes, both trying to "interview" you, which may have been what sparked the fight.
A couple of specific behaviors flag warnings for me in this case. One, the obvious ignoring of social protocols by approaching you. This is pretty self-explanatory; a man (and certainly not two men together) does not approach a strange woman travelling alone on the bus, unless he is in some way invited to do so by her. This is clearly going to weird said woman out, and the fact that they did not see or chose to ignore this social protocol says nothing good about them or their intents.
Two, the "you're scaring her" comment. This is a behavior called "forced pairing"; that is, behavior and comments which indicate a level of familiarity which does not exist, attempting to create a bond between you. Sometimes, the easiest way to create rapport is by acting like you already have it, and many predators use this to their advantage.
Lastly, there's the frequent attempts to force (or persuade) you to do small things; give up the headphones, take the token, take the money, accept physical contact...see the escalation there? From doing a favor for them, to engaging in business with them, to personal interaction. That's an escalating interview, and it's an interview you don't want to pass.
It sounds like a botched interview to me; one or both of these guys was sizing you up for victimization (in some way, couldn't tell you what they intended) and they messed it up or got distracted, probably due to their intoxication.
My advice; give no ground. With predatory or manipulative behavior, there is no place for kindness or submissiveness. A stranger asks for something from you, anything, simply say "no", firmly but not aggressively. This serves a very important purpose. If they're a good (albeit strange or socially awkward) person, they'll back off. If they're not a good person and are attempting to manipulate or otherwise victimize you, this simple no-nonsense refusal will either shut them down (90% of the time) or force their hand, making them become more openly aggressive. When that happens, it's time for the pepper spray and/or screaming for help.
No, humans absolutely do not get into hierarchy spats like dogs in a pack, but we get into hierarchy spats like monkeys in a troop quite frequently.
That's a closer metaphor, anyway. In short, if you look at the reasons animals engage in violence, and the reasons humans engage in violence...you might be surprised to learn that they're nearly identical.
If you're interested I can suggest a few good books on the subject.