On our last two trips to Jakarta (one with Lion Air and one with Garuda) my wife's luggage was ransacked and an old phone was stolen.
Security in Jakarta confirmed that this happens (again) frequently on flights from Denpasar.
The suitcase was locked, but the lock was forcefully opened damaging the suitcase as well.
Garuda replaced the suitcase. Lion promised to do so, but didn't in the end.
A friend of mine had his luggage ransacked on a flight to Surabaya recently.
So, be careful when flying domestic out of Denpasar and don't put anything valuable in your suitcase.