When a trade-route is broken by an enemy army taking one of your ally's provinces, road cut off, you get -25 for Dishonoring Treaties. That's a bit off though.
In my first game, where I never broke any alliance, and always supported my allies in wars, I got -100 to some factions for some reason that never diminished. Some of the others hit me with -100 as well, but at least for those it diminished over time. What caused this I do not know, I suddenly noticed when I was going to do some diplomacy.
So, there's something off with how this works it seems. There was a similar issue with ETW very early on as well, but it got patched not long after.