What stood out for me were a) the edges, and b) the dissimilarity in the colours. For the bright light under the islet, it was clear you cloned part of the river over the light (and my guess is the patch of river to the right of the first distinguishably single tree). The gray didn't belong in that spot, which was all black or red/yellow/orange. The same with the hat wearing tree -- it was a orange and black blob (with round-brush edges) pasted into the middle of a blue-white light.

To fix (a), the best option is to use a brush with feathered edges, rather than a hard edge (i.e. has greater transparency around the edges, than in the middle of the brush), so that the edges of the covered area are blended into the surrounding pixels. To fix (b), I'm not sure what to suggest, other than making a better choice in your clone source.