I suspect the darker color is due to being from an extract recipe. Extracts have already been boiled once by the manufacturer, so you're basically boiling a second time when you're reconstituting your extracts. Extract brewing is very difficult to pull off without some carmelization occurring that darkens the beer a little.
Many extract brewers will do late extract additions. Basically they'll only put about 1/3rd of their extract in at the beginning of the boil and then they put in the last 2/3rds with about 15 minutes left in the boil.
Don't confuse this with a partial boil late extract addition though. Brewers who do partial boils because of a smaller boil pot, will do the 1/3rd addition at the beginning of the boil and the 2/3rds addition at the end to get better hop utilization. A secondary result is less carmelization with late extract additions. If you want the carmelization on a full boil extract recipe and the slightly darker color that comes with it, you can put all of the extract in up front. If you want to avoid carmelization (such as in a blonde ale, where the color is more important to you), then late extract addition will help with that.
To add all of the extract up front or add some later in the boil is a way for an extract brewer to get some control of the final product.
I hope this helps you!