Conduct your inspections during business hours in daylight. There is no reason to inspect a property in the dark with a flashlight. Lets say the burglar alarm went off in the middle of the night. Why not just let it go off and investigate in the morning? If the property is vacant and properly insured, will you lose anything?
Discuss the situation with the local police. Tell them that you have found people on your property who are not supposed to be there on occasion. Ask if they can help you out when the alarms go off.
There might be different opinions here about this, but I think you should let your presence be known before going inside. Honk the horn in the driveway, knock on the door and ring the bell, yell inside asking if anyone is there. I think most people would try to run out the door before you get inside.