The message from future Barry says that a war is coming and present day Barry is not to be trusted. The war is the war with the dominators, and the team not trusting Barry is what will help them win. Because the team had a miniature falling out with Barry, he and Oliver ended up staying behind when everyone else went to fight the dominators. The team (minus Barry and Oliver) were hypnotized by the dominators, and if Barry and Oliver hadn't stayed behind, the would be too. The only reason Kara, Sara, Thea, Diggle, Mick, Ray, Jax, and Stein were freed from the dominators control is because Barry and Oliver were able to free them which wouldn't have been possible if the team had trusted Barry.