That is a planet passing between the camera and the sun. Not the earths moon. Viewed from earth the moon almost exactly matches the size of the sun during a lunar eclipse.
It is not a transit viewed from Earth-but an Off-Earth view, hence the size difference.
From the transcript:
"The images have an alien quality," notes Guhathakurta. "It's not just the strange colors of the sun. Look at the size of the Moon; it's very odd." When we observe a lunar transit from Earth, the Moon appears to be the same size as the sun—a coincidence that produces intoxicatingly beautiful solar eclipses. The silhouette STEREO-B saw, on the other hand, was only a fraction of the sun's diameter. "It's like being in the wrong solar system."
The Moon seems small because of STEREO-B's location. The spacecraft circles the sun in an Earth-like orbit, but it lags behind Earth by one million miles. This means STEREO-B is 4.4 times further from the Moon than we are, and so the Moon looks 4.4 times smaller
Pretty cool video - I am confused by the angles though. The moon is obviously directly in between STEREO-B and the the sun. With the moon being about 240,000 miles from the earth, and the apparent size of the moon being about 1/5 the apparent size of the sun, it indicates that the distance of the ship to the moon is about 1,200,000 miles. The article states that STEREO-B lags behind the earth in it's orbit by about 1,000,000 miles, but this would never put the moon directly between the ship and the sun. The angles to me more indicate that they maneuvered the ship to be about 1,200,000 miles farther away from the sun, lagging only 240,000 miles behind the earth, so that they could see the moon pass in front of the ship as the moon is at a right angle to the earth-sun line.
They mention a maneuver to make this photo possible - perhaps the maneuver pushed the ship into a slightly elliptical orbit to move it out from the sun and closer to the earth? But as the ship moves farther from the sun, it will move slower than the earth, and not catch up... Sounds like an energy intensive maneuver.