I bought an organic yellow bell pepper today. When I cut it open I found small brown spots inside. The outside looks fine. Is it safe to eat? 
Yellow bell pepper with brown spots inside
food-safety
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There are two types of razor clams. Since you are in the US according to your profile, I am guessing you have the type from the Pacific Northwest, which look like this (picture from Washington Fish and Wildlife):
It is normal for the razor clam to not completely fit into its shell; in particular, the digger or "foot" will extend from the shell.
According to Piscatorial Pursuits (I couldn't make that name up):
The neck tips are very tough and give off a very strong scent.
The Washington Department of Fish and Wildlife has a detailed page on cleaning and preparing the clams, with pictures. Note that they indicate (emphasis original):
During cleaning, you may find small "pea crabs" or flatworms inside the body of the clam. NEITHER OF THESE AFFECTS THE QUALITY OF THE RAZOR CLAM MEAT.
A quick google brought this:
In this case, the brown ones may have been closest to mature or viable. When fully ripe, most peppers seeds are supposed to be brown or tan. not white.
In my experience, peppers with brown are just old and withered. They are safe, just not as tasty. Unless the brown thing is mold, in which case they may be poisonous.
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Best Answer
Same texture as the rest of the pepper? ie not raised slimy etc? My guess is sunburn from it's earliest stages of development if from desert or frost if from temperate climes.
At any rate, I have eaten imperfect peppers all my life.