**Trust and not knowing the Intent of someone else**

If you think about it for a minute, everything little action you or everyone else is doing is always happening because he/she/it gets at least a little value out of it (or hopes to get some in the future). This value doesnt need to be much, it can be as simple as "feeling good because i do it".

If you now think about why Entities actually do what they do **in the long term**, you will also notice that it's not only "a little value". But it's always out of selfinterest. I will just cite yourself: "any action that increases our chances of survival and reproduction as a species is rewarded by our brains and any actions that decrease those chances are punished"

That's nothing anyone can really avoid. That's just like it is. Now here comes the problem why your described civilisations will (from my point of view) still be in war:

They don't know another good enough to correctly judge if a action a different Entity does is actually good or bad for the observing Entity.

Or in other words. They actually can not know why the other Entity is doing/saying the things they observe. 

So if they do not blindly trust in the "good intent" of the acting Entity, they will feel agressed by some or the other action.

You could try to avoid that for example by:

1. Making all the Data of the Universe known by all Entities. So they can predict the outcome of any action with 100% certainty.
2. Linking the Brains of all Entities, so they always exactly know why the other Entitie is acting like it is (think of Borg or Zerg)
3. Making all Entities to behave in "vulkanian" fashion. If all Entities assume best intent in all actions they observe and start their conversation based on this action, using pure logic. Conflict can be avoided.

All of those 3 have one common issue. Evolution means mutation. Mutation means there will be some Entities which behave differently. Those could still impose a threat to the overall population.

But actually this would make for some very interesting stories. Because no one would know why this "mutant" is acting like it is.