My Mutual Defence Pact Ally occasionally attacks my warships

[Johnnycai]

Can anyone help in determining why this is happening?

Later game, ROTS, at war with Shak and mutual defence with Ancients.
Whenever a warship(automated) wanders into an Ancients system for refuel or because they are escorting, they are getting smacked by my Allies. The Ancients homeworld is stacked with bases and ships so I dont even get the warning until they are mere fragments and dust.
Also, occasional Ancient fleets will come into my systems and begin shooting at a warship and then my ship/ships will return fire until retreat or death. This happens occasionally but frequently enought that am now checking on it. It is draining resources and forcing me to watch for inbound 'friendlies' to my systems. No private ships are being whached by them even if they goto their homeworld.

Further info, the ships getting hit are native to my human designs (not Ancients or other races design).
DiploScore to Ancients is good +35-55 range.
No followup warnings or cautions when our ships engage. Ancients are NOT telling me to get out of here or else or stop taking my mining posts . I have colonized some of their planets in their systems where they were only mining them...some of these new colonies were avg quality and with luxury/rare resources.
Is this a bug or in response to my colonizations?

[J HG T]

This has happened to me once or twice while having FTA and MDP. Not with Ancients but with Zenox. Excellent relations on both times, around +50.
I'm not 100 % why this happens, but from what was discussed on the boards it may have something to do with AI provoking you to open war. Considering this, Ancients behavior may be left-over from basic race settings as Ancients are just slightly "modified" normal race. 

Usually this happens with aggressive races that hate you. For example, in my last game the Haakonish (Furious, -100) would shoot any of my military ships that entered their systems without warning and even chased my spy/radar ship through couple of systems before stopping. 

[cookie monster]

This will happen when you have disputed bases/mining stations.

Buy or sell all disputes to get a clean sheet.

I once had a game where it started with the Kiadian's in my home starting system, they would attack my ships and mining stations without warning.

The reason, because we shared the same territory.

[Data]

This will happen when you have disputed bases/mining stations.

This is very important for the AI. No matter how many good things you have to offset this (even if you provide them zentabia, loros and korabian) it will still make a big thing out of this factor.

[Johnnycai]

Thanks all for the input, I will check this at my next chance.