It could be normal for them to be dark brown. Manzano seeds are Black. But typically, you will find the vast majority of seeds to be a very light color. (I am color blind, so for me to pin a "color" on them would not be right), but good seed is typically very light colored and when dried. If you harvest them from ripe, but not over ripe pods, they should be very clean and light colored. If the pod is over ripe or the seeds have started going bad, they could get discolored.
The only way to tell for sure is to dry and then plant a few of them to see if they germinate. You could use the paper towel/baggy method for this purpose.
Good luck and next time you should post some pictures of what you are talking about. It makes diagnosis a lot easier and accurate.
Good luck,
Bruce

so Bruce, if you're colorblind, how do you know when your peppers are ripe?

hahaha, I guess I am not 100% colorblind. But telling the difference between colors is really tough for me. Especially shades of colors. I have a tough time with real dark colors (black, dk blue, brown, red, etc..) and other colors that have the same shading. I have been diagnosed as "color blind" several times. I flunked the US Army Physical color blind test. it limited me greatly to what jobs in the Army I was eligible for. I wound up copying Morse Code broadcasts in Military Intelligence..haha. Anyway, a lot of times, I call something a certain color and others look at me like I am nuts. I have come to know what "colors" or color ranges that I am not seeing correctly and try to limit my labeling of those colors. My wife was using two colors the other night on her bingo card and I could not tell the difference between the two. They were Pink and "Teal". ????
It makes me wonder just what I am missing when I see a beautiful fall sunrise up here in the North. I tell my wife to check out all the cool colors and she starts naming off colors that I simply cannot see. It still looks cool to me, but it makes me wonder just how much real "color" I am missing out on in this life.

As far as ripe peppers goes, I can tell the difference between Orange and Red and Yellow and Red and because they are significantly different in shade. Some shades of Yellow and Orange are much harder to see the difference in.

Here is an online color vision test. I flunk it all to heck. People make me feel stupid when I tell them I cannot see a number in the circle of dots. But I cannot.
Bruce

Here is a link that might be useful: Color blindness test

Bruce,

I feel for you buddy. It would be rough not being able to see colors, and listening to morse code had to be almost as bad as getting beat up by the Marines in the e-clubs every night. Just joking with you Bruce, you brought back alot of old memories. The morse code thing though, it would have driven me nuts listening to that

Scientifically and philosophically, colors are human perceptions and do not really exist. What somebody sees can be different from what somebody else sees. Maybe what I know as "RED" is not red. But because everybody calls it "RED" I also call it red. I understand that being color blind ( as Bruce described himself) is a different matter.What hits our eyes are just various waves with varied wave lengths. Then our mind translates them into colors. There are a lot of waves out there that we cannot even see.
Rumi , the great Persian Mystics poet has a verse which translates like this:
You had a glass in front of your eyes ;
That is why the sky you see is blue.
Why we perceive a tomato as red ? Because it absorbs all the wave lengths in the spectrum and reflects back just one wave length that we identify it as "red"

OK. Back to subject:
I was in an Indian grocery store today looking to buy some spices (Chutney powder). I also bought a bag of dried red chili, called "Cashmiri". It is a pleasantly mild and flavorful pepper. I grind and uses it in place of store brand Paprika. Anyway, I thought why not grow it next year !. So I am soaking some seeds and I will test germinate them in paper towel/baggy. Talking about colors, Cashmiri pods have a nice dark brown appearance. almost chocolate like. But when ground looks light red.

BTW: I took that test and passed.