I have a hard time believing someone happened to be out in the woods at the exact same time Brandon was lost and killed him. Sure, it's possible, but that generally tends to be limited to movies. In reality, it's extremely rare. I had read there was an abandoned farm nearby, was this the only farm in the immediate area? (my memory is foggy on this case and I couldn't find much info about farms except for the abandoned one)
IMO I don't think his phone battery dying was the reason he said "Oh, s***!" If he had the phone up to his ear, he wouldn't have known it had died until it had actually powered down, so his father wouldn't have heard that exclamation because the phone would have shut off immediately and not given Brandon enough time to be heard. Essentially they would just be talking as normal and then suddenly silence. Does that make sense?? (probably not!) I guess it might be possible if he was using the speaker or his phone produced a loud noise to indicate the battery was low, but he never mentioned this to his father on the phone, did he? (No "I probably won't be able to talk for long, my battery is low" or anything like that)
More importantly however, his phone didn't actually disconnect after that exclamation, he just went silent and wouldn't respond. His father decided to hang up and call back several times but the phone wasn't being answered, so it was still turned on and receiving calls but no longer within Brandon's reach.
I'm going to go with the cliché theory and say I think he fell into the river (or had some kind of bad fall, at least) causing him to say "Oh, s***!" on the phone, but I don't think he drowned in there. The search dogs jumped into the river and then back out at a different point, so IMO he fell in, dropped his phone in the process, managed to get out and - with soaking wet clothes in cold weather - tried looking for somewhere he could keep warm as he began to succumb to hypothermia. Why he hasn't been found is a mystery, but with it being a rural area it's not unheard of to have someone go missing for years before they're eventually found; sometimes the dense undergrowth or overgrown grass can conceal a body well, even more so skeletonised remains.