The Xindi were told by the sphere builders that humans were going to destroy them and in one of the episodes Degra explains that they did show them a "vision" of the future in order to convince the aquatics. It's also explained that the sphere builders were thought of as guardians since they helped bring peace to the warring races.
I think they went on to say that the first probe overheated or something happened to short it out before it was completely finished so the destruction was probably thought to be much larger than it really was when implemented. Then they figured, we'll just build something bigger and test it this time before we just send it off to kill.
I think the original arc was supposed to really focus more on the TCW and how humans really changed things up for future races.
Again it would have made more sense if say the Xindi had found a probe sent out into space by Earth hundreds of years prior and found its way into the Expanse, they are able to decipher the data and think its some sort of warning of some immanent danger, they research what they can on humans on see that we have had 3 World Wars and have manifest destiny syndrome always wanting to conquer new frontiers.. The non humanoids feel like humans resemble the humanoid Xindi which helped create great mass weapons during there wars and feel the humans would do the same and act.