Replying to HDR in GIMP 2.8

I'm new to photography and just bought my buddy's used T4i. I went hiking the other day and tried out exposure bracketing. I do not have photoshop so i've been using GIMP to edit my pictures in. The only decent way i've found to create composite HDR images in GIMP is to manually compile different layers together. For the sky i cut out a dark threshold and overlayed it over the lighter exposed cliffs. My problem is that i get these weird lines around tree branches that the threshold didn't take out (picture 2). Any thoughts on how to fix this? I realize that a steadier tripod and better lenses will improve the sharpness and image quality.