If that one spot of orange is all there is, don't worry about it. I worry more about the membrane. It is supposed to be up on the wall from 6 to 12" and your wall cbu applied over it before you begin tiling. It appears your walls may be sheetrock. Is that so? If so, they need to be removed and replaced with cbu, or covered with Kerdi prior to tiling.
As far as low spots, unless you want to tear it all out, there won't be too much you can do about it.
As far as low spots, unless you want to tear it all out, there won't be too much you can do about it.