Characters are shown viewing the eclipse from various locations (California, upstate New York, Haiti and somewhere in the American Midwest) at apparently the same time. However, a total eclipse lasts for only a few minutes over a very small portion of the earth's surface and in an arc which would make this impossible.
A pivotal prop in this episode is the Japanese comic that Hiro uses to follow their actions. They bought the comic in Japan, and it's in kanji, but the pages go left-to-right, western style. Japanese comics page right-to-left - when looking at the cover, the spine is on the right.
As the Moon is nearing one degree (one Lunar breadth) of the Sun to its right, it is shown as a First Quarter Moon (right-half illuminated). It should be a New Moon (dark) as it is during all solar eclipses as the Sun is nearly 400 times more distant from the Earth than is the Moon.
At several points during the eclipse, when it's nearly total, the lighting is dim, but exterior shots of reflective surfaces (such as the hood of Noah Bennet's pickup) show a fully illuminated reflection of the sun, showing that these scenes were simply shot with a lens filter.