Well it's definitely time to separate them ASAP. Sometimes they are fine for a while, or rather they appear to be fine for a while, but if they are truly a male and a female both over 2 years old and they aren't head bobbing,
black bearding, or breeding, and they are sleeping on top of each other, he is so stressed out right now he's either not eating or he's physically ill. He's extremely thin, to the point he looks very unhealthy, especially for a 2+ year old male. It's not odd at all that the female is the dominate one, especially if she's bigger than he is, or it's possible he was sickly or weak and she took advantage of it. Either way, their breeder should have never, ever, ever told you to house a male and female together! They know better than that, they just wanted to sell you two dragons, because there is no way they house their males and females together. Under normal circumstances if they were both healthy and of normal size there would have been breeding, aggression, injuries, possibly a death by now. But it's obvious just by looking at the poor guy that he's stressed out and needs to be by himself from now on. It's best if they never even see each other again, and you need to remove her and allow him to stay in his current enclosure, he's way to sickly and stressed to deal with relocation stress too. She can handle it. If I were you I would get a big plastic tub and a second clamp lamp and a second basking bulb, and put her in it tomorrow. She can go without a
UVB light for up to a week without issues, he can't. And you need to stack them or keep them in different rooms from now on so they can't see each other anymore, if they can the male will continue to stress and not eat. This isn't uncommon to see or hear about, it's just sad and frustrating. It's not uncommon for breeders or pet stores to sell 2 at a time and tell the buyer that they can live together, not even mentioning the fact that they're naturally solitary reptiles and the only bearded dragons that have ever really been housed together successfully are multiple females, and even that doesn't work out often. So please, get her out of that tank, out of his sight, and give him some special attention, lots of good food (I'd actually offer him more live bugs than he usually gets, he needs the protein, he's really thin and not well looking)...
As far as his beard, the grey spots look exactly like shed, but as far as the black spots I can't see them well enough to tell...are the black and grey areas raised or like "growths" or skin hanging or growing off his beard, or are they simply coloration changes? I can't tell, I mean if I could see him up close it wouldn't surprise me if they were bites or scratches from the female, but it doesn't look like that. If you can describe what the spots are like a bit more in detail, or maybe get some close ups it would help. Like I said, the light grey spots appear to be shed (shed often gets stuck on their beards, it's a bit weird for them to shed that area), but the black spots I'm not seeing well enough to even guess at this point...are you sure they are actually black and not very dark red dried blood?