You know what I’m saying? I’m saying this is bullshit. If a sixteen year old Dean Winchester came face to face with a werewolf like that, he wouldn’t be alive. The werewolf wouldn’t grab him from the forearms. He or she would bite him and claw him till he was dead or too weak to move.
So yeah, this isn’t a werewolf. That’s just John.
Friendly reminder that Dean didn’t ever personally encounter a werewolf until Season 2, 11 years after this episode.
Actually, according to Dean in 2.17, Heart (the episode with Madison the werewolf), the boys have encountered a werewolf before—the exact line he uses being, “I’m sorry, man, but what about ‘a human by day, a freak animal killing machine by moonlight’ don’t you understand? I mean, werewolves are badass. We haven’t seen one since we were kids.” So, no, that can’t be used as evidence that this was physical abuse on John’s behalf—unless, of course, Dean is keeping up the excuse of the bruises being a werewolf’s fault even eleven years later, though his usage of the word us rather than Iimplies that Sam was there the first/previous time they faced a werewolf.
However, I wholeheartedly think that the bruises were John’s fault. In the live-action version of Supernatural (shh no one mentions the anime shhhhh), werewolves are characterized by their superior senses, their regenerative abilities, their fangs and, most importantly in this situation, their claws and primal, animalistic mindsets.
If a werewolf were to grab Dean by the arms like that, there would be abrasions left behind by its claws—and that’s assuming a werewolf would even be impractical enough to grab him by the forearms.
The logical motion for attack would be to grab his shoulder(s), sink its claws into his flesh to get a good grip, and yank him closer to bite him in the crook of his neck if it had the idea of converting him in mind. Otherwise, it could simply just tear a bite of his throat out and have him for dinner.
There’s no conceivable reason for a werewolf with the intent of overpowering and possibly killing Dean to just take him by the forearms (without using claws to get a better grip, no less!), because that would put a gap between them and subsequently give Dean a fair chance of pulling away.
Dean bears no cuts on his face from the werwolf trying to disorientate him, and we haven’t been shown any other injuries that would suggest a struggle—this is especially interesting, considering that the bruises are on both forearms and therefore suggest that Dean was facing the “werewolf” when it grabbed him. So it’s not like he was caught off-guard like Madison had been.
These injuries were made by a human (probably male since we can’t see any nail marks and men tend to keep their fingernails clipped shorter than women, though that’s just a guess) whose intent was to hurt Dean—probably out of anger—but not to harm him fatally or to the point that medical attention would be required.
So, the possible sources for the bruises could be: the deputy who brought Dean in (he had a black eye which could imply a struggle between the two), a fight with another man, or John.
When Sonny asks whether the deputy gave Dean the bruises, Dean outright laughs at the idea, obviously not thinking very much of the deputy (earlier, he calls the deputy slow, in regards to him having left the deputy with a black eye). A fight with someone is possible, but it seems unusual: as earlier stated, Dean has no injuries on his face. That could imply that he won the fight, but I’d assume he’d be eager to boast of his victory, considering his character.
And who does that leave looking guilty? Ding ding ding, you got it: John Winchester.
I just rewatched the scene to pay attention to the body language between Sonny and Dean when Sonny asks if “his old man” had left him with the bruises. Now, we know Dylan Everett, who played young!Dean, was very dedicated to delivering a believable performance; he watched the entirety of Supernatural (in a single week, if my memory serves correct) and studied Jensen’s portrayal of Dean so he could mimic it—which he was very successful in doing.
With that amount of dedication and hard work, I’m quite certain that he would’ve put a lot of thought into every single one of his scenes, especially one where possible physical abuse is brought up.
Back to the point: when Sonny sees the bruises, he asks, “The deputy do that?” Dean scoffs and averts his gaze to the right of Sonny’s face. Then Sonny asks (paraphrased) if they were caused by Dean’s father.
At this, Dean enunciates, “Werewolf," almost sarcastically, and skirts his eyes over Sonny’s face to look just left of it; however, he doesn’t actually look at Sonny while doing so.
There are a few moments of silence in which Sonny studies Dean’s face while Dean refuses to meet his gaze, then Sonny nods, says, “Okay,” and looks down to unlock the handcuffs. It’s at this point, while Sonny is focused on the ‘cuffs, that Dean looks at his face for the first time since the bruises were brought up—and this is the look he has on his face:
(Cap grabbed from here; sorry it isn’t the highest quality.)
The moment Sonny returns his attention to Dean again, Dean immediately leans away, regains his air of arrogance, and changes the subject.
This scene was full of very purposeful body language—and, if you ask me, that would be kind of odd if it was simply there to reference a monster we didn’t even see—a monster that had no connection to the case in the present scenes or young!Dean’s shot at a normal life in the flashbacks. There’s no reason to pack this much subtext into a pretty much entirely irrelevant scene unless we’re supposed to look into the subtext.
There are several implications that John was physically abusive toward Dean (not Sam, though; I’m assuming Dean acted as a buffer between the two and often took the brunt of John’s anger so as to protect Sam)—for example, Dean’s expression in Dark Side of the Moon as he recalls John’s reaction to finding out Sam had run away on Dean’s watch.
Something on a broader basis that contributes to this theory is how Dean tended to adopt a sir yes sir! attitude around John, while Sam would challenge him. If Dean did act as a buffer between John and Sam, like I said earlier, Dean would obviously be more aware of how far John could go and therefore be more scared of the consequences of taking John on/disobeying him, while Sam would lack the experience to make him as wary. (Also, I vaguely recall Sam saying something about John being a mean drunk, though I’m not certain and don’t have a source so I’m not going to use that as evidence.)
TL;DR: Yeah, I’m about 130% sure that those bruises are the courtesy of dear old John Winchester, so I’m sure as hell not nominating him for Father of the Year anytime soon.