You don't need to use a pre stain conditioner with oak, it isn't a blotch prone species. What did you use? Red oak is "dotted" so to speak, little dashes that indicate the direction of ray growth. When you are trying to "cut with the grain" you use these to identify the direction to feed the lumber into cutters. The tip of the pencil is pointing to these in the picture. The annual growth rings give that cathedral appearance that many call "grain" on red oak. In the pic, the rings run opposite the rays and you would feed this particular piece eraser first.
Red oak is very prone to mildew growth. This starts as black dots. A little moisture on the lumber can start it. It's always a good idea to sticker lumber that sits over night, not place boards on top of each other, so air can circulate. This technique is mostly used to prevent lumber from warping since the surface exposed to the air will dry and the surface that isn't exposed will not. Mildew can be identified by wiping the surface with bleach. It will come off, but it won't sand off.