It's because of the old SEA conflict called Konfrontasi. The first president was a communist sympathiser, so when the UK tried creating the Malaysian Federation. The communist party in Indonesia (PKI) opposed that Idea even though the Indonesians were mildly supporting the federation. In Brunei, they were slightly reluctant to the union since they wanted to keep the sultan's power and rich oil. But when some of the politicians in Brunei wished to oppose the unification. The opposition then launched a rebellion that Indonesia allegedly funded and trained ( They failed and fled to Indonesia ). Then the coalition condemned Indonesia, and Brunei ended up not joining Malaysia. They also then created an agreement that the people of Malay needed to choose if they wanted to enter Malaysia. They slightly disregarded this agreement and went to sign the federation in Britain. Indonesia then feels this federation signing is too hasty and illegitimate while insulting Indonesian independence. So the first Indonesian president launches an attack using volunteers that disagree with the federation. After the volunteer coup, a race riot happened in Singapore, and they blamed Indonesia for staging it. Malaysia then complained to the UN, but Indonesia countered it with that the race riot occurred because of Malaysia's inequality. The US then interfere with the Confrontation, and Indonesia then Join the Chinese communist. Indonesia then withdrew from the UN while uniting with Beijing. This causes some economic problems in Indonesia. Then a coup happened in Indonesia, and the first president was replaced with a president who hated communists. A mass genocide occurred in Indonesia, killing around 500,000 - 3,000,000 people connected or suspected of communism. The Confrontation ended during this coup, and Indonesia rejoined the UN while leaving its communist allies. The coup happened due to the US CIA's interference and help by supplying them with radio and material since the first president at that time was a communist sympathiser. Singapore then parted ways from Malaysia and started its national service to protect itself. Some people say this is all the CIA's plan to change the Indonesian regime to a non-communist since this happened during the cold war, and the US failed to attempt to blackmail the Indonesian president.