In the first book of the Geralt saga, Blood of the Elves, the dwarves are on a hoax convoy mission set by the king to test their loyality. The thing is, he lies about the fact that the dwarfs are sent out because the Scoia'tael would have a good releationship with them and so wouldn't harm them. However that does make sense to me. Of cource they have a few humans with them like Geralt, Triss and Ciri but would you kill potential traitors of your enemy? So why did they do it?
2 Answers
The train is meant both as a test of loyalty for dwarves and a plot to uncover a traitor in the court of King of Kaedwen. This is pretty clear - however can't remember if explicitly confirmed by any Kaedwen official- when you read the book. So attack is obviously an attempt to weaken the enemy (Kaedwen/humans) in the eyes of the Scoia'tael. That it was dwarves guarding it would fall into a category of "unhappy coincidence", and taking force disparity of the opposing forces it is most logical to adopt "shoot first, ask questions later" approach for the Squirrels...
I would point out, however, that I'm basing this answer on the original book and my memory. Translations may vary, so without knowing which it is I can't check and usual disclaimer of "AFAIR" is in effect.
There is a possibility that Scoia'tael treating dwarves as traitors. Dwarves are "aliens" too but they're trying to live with humans instead of fighting them. I think that elves rather kill them than let dwarves become allies of humans.
But that's only my opinion.
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That contradicts with the fact that some of the dwarves on the train were actually murdered by scoia'tael dwarves. Commented Oct 7, 2016 at 18:59
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3Those dwarves (scoia'tael-s ones) have even more reson to detest those dwarves that are employed by humans. Even though they are the same race, one group detest another because of different social status or different views. Commented Oct 11, 2016 at 11:49