It is very common with Alden #8 shells. In most cases, the uneven dyes are apparent only in very strong light. Brushing does not help. Some may consider it as a defect, but it is so common that I think Alden would consider it as normal. Though, I have yet to see similar issues with Bordeaux Cordovan shoes from Carmina, Vass, C&J, Wolverine or AE.
Although I agree with several of the folks here in terms of the commonality of those spots on #8, it still isn't on all of their shoes. I also agree with the fact that they are where the creases are going to form and thus will be less noticeable than if they were say on the toe. But the fact remains, that there is very low chance of it ever going away and you just spent a hefty chunk of change on them. So it's entirely up to you as to whether you are happy with them or not, if you are keep them enjoy them and love the way that they will mature with age. Otherwise return them to the Crew for an exchange or refund. Good luck!