In the 16th century, four countries(the Spainish, Portuguese, British, and Dutch) set out in search for "The Spice Islands". They brought with them many ideas and much culture. The British ruled for a short time before the Dutch took over all of Indonesia. After independence, Indonesia and its border countries decided on fair boundaries.
Treaties and documents were created to finalize it but arguements sometimes occured, such as the complications with Malaysia's 1979 map. Problems and disagreements have risen again and again between the two countries. Mostly, boundary disputes have been about the island of Borneo and maritime borders. They have attempted working together by joint-management on the fought over areas.
Another treaty was created between Indonesia and Papua New Guinea in 1986, however, not everyone agreed with it. Many dislike the law-breakers, refugees, and people crossing into Papua New Guinea. The border is poorly developed with bad infrastructure.
Picture: A map of Indonesia, showing its bordering countries