It seems dark in the carboy because the light cannot get through the liquid in the carboy as easily as in the glass, hence it looks darker. If you follow the recipe correctly, the color difference should be very slim to none.
There's also tendency that the beer will turn darker at the end of the fermentation than it is at the start; this is due to yeasts flocculation. Because there's not enough yeast particle to bounce the light back off, it looks darker. It will look a lot lighter in the glass.
So, if the recipe is followed correctly, you dont have to worry about anything.