When I run for over 30 minutes, the toe next to my pinkie bleeds on the top-side by the knuckle. Why?

Several things. Your toe may be elevated and being rubbed on the inside of the shoe creating bleeding.
Likely friction. From the shoe and possibly bunching up of the sock. As you run, the foot jams forwardinto the toe box of the shoe. It may be very easy to prevent by wearing a band aid over the toe when running.