Is it only in the course that you see 2 admin blocks? This may mean one block is from the system (the front page) and one was added directly into the course.
Turn on course editing - click "configure" on one of the two blocks. You will see if the block was added system wide or directly to the course. Keep the block that says "system" and delete the block that says "course"
Turn on course editing - click "configure" on one of the two blocks. You will see if the block was added system wide or directly to the course. Keep the block that says "system" and delete the block that says "course"