Sometimes the inner tube wants to lay out very flat and bridge the lips of the rim, making it hard to impossible for the tire's beads to set properly on either side of the valve. You won't really see or feel the tube because it's on the lower hump area of the rim's shoulders. If your tire is ever sticking up slightly or bulging around this area, then deflate the tube all the way and gently work the tube up inside of the tire with something blunt like your tire levers. It's nothing you did wrong or incorrectly, it just happens sometimes.