Well, as the old joke goes, if it hurts when you do something, you should probably stop doing it!
Some races don't take too kindly to others helping them out. The Andors, well known for their pacifism and generosity, are typically targets for this since a lot of their deals help other races out. I don't believe this sort of resentment is true with all races though, but I haven't experimented enough with the game to figure it all out yet.
That said, there are a few ways to help boost relationships between two races. Under "Friendly Actions" you can always dispatch yourself to improve relationships between the two, though that only goes up to a point (50 influence?), and that does take time. By far one of the best ways though is setting up a trade route. Trade routes seem to build up a good amount of influence between the two races over time. The only issue is that some races don't have the option to broker trade routes (Burlasts come to mind as one example), however, I think you can still have the other party initiate a trade route with them? (I could be wrong about this).
