I'd never secondary an IPA. IPAs need to be drunk fresh.
That being said you can't judge the color of a beer from bulk storage. It will always look darker in bulk than in the bottle or glass. Without knowing anything about the recipe it's impossible to say what color it should be but the only way you could have darkened it is by boiling WAY to long which would reduce your volume. Or you scorched it on the bottom of your kettle and will have some serious off flavor.
I misread your post, thought we were discussing an IPA but I looked up the Carmelite Ale and I see it's a trappist triple and a partial mash kit. With extract brewing you'll find they're always a little darker than with all grain. Holding your extract out until late in the boil can help keep it a bit lighter. If you did a partial boil with extract in the kettle I'd expect it to be darker than the predicted SRM but it shouldn't change the taste profile of the ale much unless you scorched some of the extract as I mentioned above.