How visa days are counted? (Malaysia)

In-country days are counted as calendar days not 24 hour periods. The day immigration stamps your passport starts the count. It doesn't matter what time you enter, be it 1 am or 11:59 pm, that arrival day is counted as one of your 30.

The allowable stay ends at 11:59 pm on the 30th day (18 June in your specific example).

This in-country 'clock' revolves around when immigration stamps you into or out of the country, so one could conceivably fly on day 31 at 4 am, as long as they cleared immigration before midnight. But in countries like the USA where there are no exit formalities, then your clock stops at takeoff, so you need to fly out on the last day.

Pic - Sample of a VISIT PASS in a passport page. Includes the Return (or Outbound Air ticket sighted) and noted in the immigration stamp.

1. The day one enters Malaysia is taken as DAY 1. Must exit before the 30th Day or be regarded as "Overstay". Overstay in Malaysia is a Criminal Offense under Immigration and Civil Laws. Overstay even 1 day is overstayed.

2. It is prudent for a tourist to planned a 28 days visit to avoid breaking Immigration Laws. There is no excuse for missing flights, that it why a return ticket is compulsory as one of the minimum requirements for entry into Malaysia. Malaysian counters at Airports or Land Border Checkpoints are not allowed to collect any fines or moneys. Any overstay will have to go to the nearest IMI office/centers to pay fines. You would not be able to board the flight out of the country even for 1 day overstay.

3. There is no such thingy as "Visa Days" in Malaysia. A visa is to enter and Visit Pass (as shown in the above pic) is stamped into the passport pages to allow the tourist to live in Malaysia for a specific period of time. Please take serious notes that the "visa" systems in Malaysia, Singapore and Thailand is different from most of other EU countries.

EDITED

By Sunday, June 19, 2016 at 00:00 you should leave Malaysia. Which means June 18 is the last day till 23:59.