Hard to tell from your description but it could be retained shed on the toe(s). This usually can be removed by soaking the dragon in luke warm water for 10-20 minutes (make sure the water isn't too team, offering a rock, your hand or a rolled up washcloth for a place the dragon can rest against is good). If you do see unshed skin around the toes, carefully remove with tweezers. If left on, unshed skin on the toes can cut off circulation to the toe, resulting in it dying and falling off (or gettin infected and causing other problems).
Another thing it could be is the toe was bit by his cage mate. Any open wounds can be treated with an antibiotic ointment (any without painkillers added) to prevent infection. Also remove any loose substrate from the cage (baby dragons should really be on papertowel or newspring anyway, to greatly decrease risks of impaction on sand etc).
The last thing I can think of that may cause demormalities in toes (other than a genetic defect) would be a calcium defficiency (ie MBD). Make sure you have a good UVB bulb that is less than 9 months old (of use). If you have one older than 9 months, then it's best to change it. THough visible light will come from these tubes for years, the level of UVB produce decreases quickly. Good brands of UVB I know from both experience and what others have said (or tested using a UVB meter, see: www.beautifuldragons.com for info on UVB outage of many brands of UVB bulbs) repti-glo and repti-sun are good.
OTher causes of MBD could be not enough calcium in the diet. Make sure you are dusting at least one feeding of insects a day with a calcium powder with D3. Babies should get 2-3 feedings of insects a day, plus offered finely chopped greens (the website below also has a great nutritional chart to help in choosing what greens/veggies are best for bearded dragons)
As an afterthought, I suggest separating your dragons now. Even if they are getting along, there is a high chance they will have to be separated anyway, once they reach 6 months of age. Since baby dragons are difficult to sex accurately, a pair could wind up two males, a male and female or two females. Two males should never be housed together as they can become extremely territorial, especially if they sense a female nearby (if you have a third bearded dragon housed separately, or decide to get on at a later date). Even if no females are present, males can fight eachother and cause severe injuries and death. There is no place to run to in a 5'x2'x2' cage one can't be followed by the other. In the wild, the dragons run to get out of the territory of a stronger male.
Having a male and female brings in the complication of the female being bred too young (females should be allowed to reach at least 14 months before being bred. 18 months ormore is better. This gives the female time to fully grow and be as healthy as she can be before putting the strain of egg laying ( not to mention having a 'randy' male pestering her constantly just to get her gravid) on her body. Though many females lay infertile clutches before reaching 14 months regardless, infertile egg laying is not as stressful to the female, providing she has all her nutritional requirements met and a lay box prepared for her to lay in.
Two females can get along all their lives, especially when raised together as babies. However, even adult females can suddenly decide they no longer like eachother after living together in 'peace' for years. Also, while growing up, one female can wind up being the more 'dominant' and get the best food, basking spots etc, while the other winds up being stressed, not eating as much and often not growing very fast (and this adds to the problem as then you have a big dragon lording over a small sickly dragon that more often than not, will die, unless separated).
With that said, it is possible to house dragons together without mishap (in the case of two females) you must be prepared to be able to separate them immediately should they suddenly start fighting. (but till you are sure on their sexes, best to separate before either reach 6 months. If you are not sure on their age, separate before you have had them for 3 months. Most breeders don't sell their dragons younger than 6 weeks old but always good to be on the safe side, hence my suggestion of separating after you had them for three months).