It's written down somewhere, but probably easier to just tell you. The Sky People only came to Earth within the last couple of years, and our first dropship was full of teenage delinquents (myself included). We landed in the middle of Woods Clan territory, but we didn't know that anyone in Earth had survived, so when we ran into scouts and warriors from Trikru, we freaked out a bit. We made mistakes and killed some of them (again, because we didn't know they were even there to kill), so when we finally got face to face with them, they were already aggressive. Negotiating peace with Grounders is really difficult, especially when they think you're just trying to make nice because you started a fight you couldn't win.
We ended up on the same side of a conflict with the original inhabitants of Mt. Weather, the Mountain Men. The Mountain Men had been kidnapping Grounders for years, turning some of them into insane cannibals and brainwashing them into kidnapping other Grounders for them, and using the rest for blood transfusions and "treatments" until they were bled dry and thrown out. They had no immunity against the radiation because they'd been hiding in the base and never built up any resistance, so they needed the Grounders to survive. They found us, took us in, and when they found out that our resistances were better than the Grounders because we had more direct contact with the radiation in space, they discovered they could give people permanent immunity with bone marrow donation instead of just blood. Instead of letting us donate, they decided to steal it from us instead, and they killed some Sky People by drilling out their bone marrow until they died. We worked on a plan that would free the Sky People and the trapped Grounders, but Lexa turned on us at the last minute and made a deal with the Mountain Men not to attack them if all the Grounders were released and the Skaikru were left behind. We ended up opening the doors to Mount Weather and flooding it with radiation to kill them before they could take more of our own lives, and then we moved in to survive the winter.
So there's bad blood on both sides. Our initial conflicts were all with the Woods Clan. We didn't even know there were more than just Trikru until we started dealing with Lexa.