To those asking, many of those with colored eyes in otherwise b/w stories are 'twitter' series or the like (pixiv, etc.)
Not all of course, it has occasionally happened for a while, but ime many of the more 'recent' cases of this have been from this type of thing. Often an artist who is releasing their own work, or producing on a somewhat 'smaller' scale.
Otherwise there are a few other reasons, but they are generally more on a case by case basis.