Most murderers know their victim, usually a close relationship with their victim.
Many burglaries, the person has been to the location and is coming back for what he knows is there.
So them knowing each other doesn't sound suspicious to me, they either had a grudge and the guy sneaking in intended to do him harm, or he was sneaking into the house to pilfer what he coveted from his friend/acquaintance. I'm sure the cops will investigate the possibility that the shooting was the result of an argument and the shooter is lying that his friend/acquaintance had invaded the home.