Carl was wrong when he thought that Jared was perfectly happy being a horse and not bothered by human values. Jared still had his sense of human values and wasn't happy seeing his father take advantage of Eric the way he was. The only reason it seemed like Jared wasn't bothered was because being Jasper caused his mind to be so relaxed that he was almost asleep.
Jared wasn't getting the full experience of being a horse. His experience was of being very relaxed. It was more like he was dreaming that he was a horse, not actually being a horse.
But watching his dad take advantage of Eric troubled him so he fought to wake up enough to do something about it. It was hard because everything about being Jasper made him want to relax but he needed to be diligent for Eric's sake.
Seeing Carl/Jake about to mate with Eric/Bonnie was the last straw. Jared/Jasper reared up on his hind legs and broke the gate down. Jake/Carl interpreted this as a rival horse challenging him for the chance to mate. Jake and Jasper started fighting but Jared and Carl realized that they were hurting each other so both boys woke up and took control of their horse bodies. They led Bonnie/Eric out to the road where the three horses ran for the woods.
As they ran, both Jared and Carl were tempted to give in to their horses instincts to mate so they left Bonnie/Eric in the woods. Jared tried to return home for the amulet. He lost track of Carl/Jake and didn't know where he was. He was sure Carl wasn't with Bonnie/Eric but maybe Jake/Carl found another mare in heat. Jared needed to get the amulet and turn human so he could fix this mess.
But as he got close to home, the desire to relax and drift away became overpowering. Jasper stood in front of his home confused about why he was out.