Um, I have no recollection of Steve putting in anything about alliances
[Pause while searching for Diplomacy thread]
Ok - here's the diplomacy rules from 4 years back - I don't think there have been major changes in the statuses. (I found it by advanced searching for "trade" and "points" in all threads from "Steve Walmsley". I could have further restricted the search to only look in "Mechanics", since that's where he tends to post new rules.) http://aurora2.pentarch.org/index.php/topic,1613.0.html
If you read the whole thread, you'll see Steve eventually lists the possible statuses (and the diplo points needed for each one):
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Neutral Military Status: -100
Friendly Military Status (Jump ships can escort the alien Empire's ships): 800
Allied Military Status: (Ships will defend the ally's ships against missile attack): 4000
Trade Access: 200
Share Geological Survey Data: 800
Share Gravitational Survey Data: 2400
Share Research Data: 6000
+++++++++++++++++++++
There are two important things to understand here:
1) Diplomacy points are NOT symmetric. The diplo rating that you see of 2200 points is your people's attitude towards them, NOT their attitude towards you. So you could be loving them (+2200), while they hate your guts (-500). In which case they would go to war with you and your attitude towards them would begin to drop as they did naughty things like dropping asteroids on Buenos Aires.
2) The best military status is "Allied". That says that they'll cover you in their anti-missile umbrella, but it doesn't say anything about changing attitudes towards someone who attacks an ally. I just re-checked the original post, and I don't see a negative modifier to damage done to allies - only for damage done to your ships/pdcs. It makes sense for Steve to put something like that in (maybe with e.g. a 50% discount) but I don't remember seeing an announcement about such a change. In addition, I'm not sure how likely it is that the two NPR would have gotten such friendly relations with each other.
So, barring corrections from Steve about how alliances behave, I think it's more likely that you've had warships sitting in a system where they had a colony, and that they had those warships on active sensors. This would cause their attitude towards you to drop, without affecting yours towards them. Eventually they would get so pissed off that they start attacking you.
John