I've only played once and only got to the classic era before I decided to restart again and put what I had learned into practice. With Auto Explore my units kept crossing into other civilizations territory resulting in them being attacked. Is there an option to respect borders when scouting? 

The auto explore really sucks, they should make it have some sort of intelligence. Avoid borders/conflict, but take curiosities and liars/sanctuaries. 

Maybe an option to be more aggressive, but by default they should explore, not suicide or start wars.

I had soldiers pop up onto foreign soil from a water tile on auto-explore. The only way  I could move them was to declare war.

Yeah exactly this. Auto Explore: Pacifist & Aggressive modes

zimmah wrote:

The auto explore really sucks, they should make it have some sort of intelligence. Avoid borders/conflict, but take curiosities and liars/sanctuaries. 

Maybe an option to be more aggressive, but by default they should explore, not suicide or start wars.