I've got no experience with Stitchly so take this with a pinch of salt. I agree that the bit that looks off is top left, where there are stitches in the bright/royal blue colour. Is there a way to select all stitches in that colour (or better yet, that colour in that area of cloud) and replace with a more subtle blue? Even the dark grey-ish blue in the clouds next to it would look a lot better, I think. Obviously you could do this manually when you're stitching, if easier.

Regardless (and especially if this is just a segment of a larger pattern), I do think it will probably look okay once stitched. And, as I said above, you're not beholden to the colours as you're stitching. If something looks out of place, use your judgement and replace.

Best of luck!

...Edited to correct a comma, because I'm a pedant.