Today is DAY 75 (31/05/2020) of the Malaysian Lockdown.
This is the latest statement on 28 May 2020 from a Senior Minister (Defence).
In Malaysia the Visa system is slightly different from the western countries. A VISA is required to enter and a VISIT Pass of 30 days is given to Indonesians.
Read the stamp on your passport "entry stamp" properly.
You have already "overstayed" by normal immigration policies. But because of the Lockdown in both countries, there is no International Passenger Flights as yet.
There is no need to apply for a Special Pass (Extension of stay) while the lockdown is in force.
Check with your Embassy. They should be opened now. If there is a need for you to go back urgently due work or family commitments, there are Mercy Flights, Chartered Flights organized by the Embassy.
Below is another statement dated 19 March 2020, one day after the lockdown started. It is direct from the Director General of Immigration.