Why did my son get cavities under his dental sealants and what do we do?

See below. Dental sealants are not an end all. They can help decrease the chance of getting cavities, but one still may. Should see the dentist.
Remove them ; fill! I have found decay under sealants the norm rather than exception. Most sealants are placed without proper cleaning (air abrasion), poorly etched, and bonded without proper isolation, and they are very thin and subject to removal by sticky foods. Even worse, when they leak, the chewing surface may appear ok but decay grows underneath them. I hate sealants! get filling ; check others seals!
See your dentist. Dental sealants on healthy teeth prevent cavities or if placed on small cavities it prevent the cavity from getting bigger. On a healthy tooth, if the sealant isn't tight against the tooth food and bacteria can get under the sealant, resulting in a new cavity. Sealants on a small cavity can prevent it from getting bigger, but the sealants won't make the cavity go away. See your dentist to treat.
Not Foolproof. Dental sealants are not foolproof. They reduce that chance of getting a cavity on a sealed tooth by about 80%. Sealants only protect the chewing surface (the most common area to get a cavity on permanent molars) not in between teeth. Sealants can also get pulled off if you eat sticky foods. Generally if a sealed tooth does get a cavity on the chewing surface it tends to be small and easy to fix.
See your dentist. Sealants only decrease the chance of developing cavities. They can't prevent them 100% of the time. If he has cavities, he needs to get them filled.