How did Puerto Rico pose a problem for the United States after the Spanish-American war

The United States acquired Puerto Rico from Spain during the Spanish American war. Now that they have the island, Washington had the problem of governing it. Washington sent generals to first govern the country. However, some of these military guys were accustomed to brutal administration and pacification of Native Americans. Many occupying American soldiers were also bad guys, mistreating local residents and causing fights. The ruling government was undemocratic, causing civil disorder in the island.