I don't know too much about grappling-- I don't know much about striking either, but more than grappling-- so someone else'll have to cover that, but dos Anjos has shown a historic susceptibility to classic anti-southpaw and anti-Muay Thai strategies. That is, he's vulnerable to an orthodox opponent's right-hand and to checked kicks. That was the entire reason he lost against Eddie and Ferguson.
Eddie kept moving around and kept himself in a good position to land a right-hand (I.E., kept his left-foot on the outside of Rafael's right-foot) throughout the fight, and when he landed it the fight changed. Rafael's really good at "walking his opponent down" and "cutting off the cage" as they say, since he's aware of this vulnerability, so the fact that Eddie was able to do that really says something about Eddie's footwork skill. Nevertheless, you compare that to what Tyron does with his right hand and it's a vulnerability.
And dos Anjos was actually winning the fight against Ferguson until Ferg' checked one of his leg kicks and he just stopped throwing it. That was one of his go-to moves against Ferguson, seeing his chicken legs, and once the check fucked up either his shin or his foot, that was off the table, and the fight turned in Tony's favor. He has pretty average-length arms for his size, so doing stuff like "setting up the kicks with punches" isn't really that simple. If he's outside of range where his punches'll actually land, the guy will be on to what he's doing and predict a kick to the leg, and if he's close enough for it, he's not only more open to a counter-shot because he's so close [and kicks, by their nature, leave you open to counter-shots, since you're standing on one leg unable to move and your hands are down for balance and a little bit of extra weight to throw], but he'd might as well focus on throwing punches since he's already in range.
He started throwing a lot of round kicks to the the body to offset it, since he trains out of EVOLVE with a whole bunch of Muay Thai champions and the round-kick to the body is just as beloved in high-level Muay Thai as kicks to the legs are (which's a sentiment you don't find in shootfighting) and you can't just check a kick to the body like you can one to the leg. But in MMA, a body-kick runs the risk of getting taken down if you're not good enough with 'em. And, of course, against a guy who placed 5th in the NCAA division 1 wrestling tournament, they can see an opening. Rafael throws 'em light and fast and he times 'em out well, and since they're to the body they don't have to be really hard fight-ending shots to do the damage and tire your opponent, so they're not easy to just get a takedown off of, but it's still something someone would see as something to be taken advantage of.
Every style and move has its strengths and faults. A jab is unanimously considered to be the single safest move in all of combat sports, and even it has extremely good ways of countering it badly. dos Anjos doesn't move his head much, but he likes to throw kicks, and head-movement and throwing kicks are two things that really do not go well together (stand on one leg and try to do a bob-and-weave.) The amount of fighters who are known for having great offensive kicking games and good head movement are very little, and the guys are usually very tall for their division (dos Anjos has a good forearm guard, though, and, contrary to popular belief, a forearm guard isn't some impotent move without large gloves and can actually provide a lot of defense.) It's not like those are things you can just change and suddenly you're unbeatable; it's not like you just stop pressing the square button or you press the square button better. If it was that simple, everyone would just change.
You figure out what you're good at doing and what you're comfortable doing, and you adjust accordingly, and you try to figure out back-up tricks or modified versions of your old stuff in case those don't work, and there're thousands of ways to do that.
