Cut and Pasted from TFA/TPA FAQ page:
Why do flavors change color?
Flavors can often exhibit color changes without any affects on taste or functionality. There are a variety of reasons why flavors may vary in color over time or between order to order. Heat, light, and oxygen exposure are the most common factors causing color changes in flavors over time. For example, take an apple that is cut fresh and compare it to an apple that was cut an hour before. What you will see is a slight change in color, but if you did a blind taste test, you would not be able to detect any flavor differences. Also, since many of the flavoring ingredients are from natural sources, crop variations from harvest to harvest can often explain hue changes. Flavoring ingredients may also be specified with a range of color from our suppliers, and these slight deviations can translate into our finished flavors.
Cut and pasted from Wizard labs:
Note on variations between batches: Over the years we have seen many variations between batches from every flavoring manufacturer. Some have been simple color differences, all the way up to reformulations of their recipes that require updating the list of ingredients. On rare occasions we may have two different batches of a particular flavoring from the same manufacturer which can have slight differences in color, smell, or taste.
Just a couple of examples of what I found on one manufacturer's site and one retailer's site. I don't know where you purchased from.
I have had rather significant color variations of the same flavor (by the same manufacturer) ordered from the same supplier on different orders. That said I have never had and entire order come in uniformly dark.
I am in agreement with the previous posters, in that I don't think it would hurt to give them a call, or shoot them an e-mail and ask. I would be curious to hear how they reply.