The first one that I remember involved Aaron Eisenberg (Nog from DS9) playing a Kazon child who was trying to earn his name. The Kazon ship fired on his shuttle and breached the hull. Chakotay and the kid beamed down to the planet as the shuttle hull breached and the craft exploded.
$$ Voyager Season 7 Spoilers below $$
The second time I'm positive of involved a season seven episode where Chakotay and Seven were in the shuttle examining the planet with the energy field surrounding it to protect the primitive people living on it. The shuttle clipped part of the field and crashed.
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A third time that might have been Chakotay's fault was an episode where there's a shuttle crashed on a gloomy world. Janeway is having out-of-body experiences the entire time. I don't remember if he was piloting the shuttle or if Janeway was.
I think Chakotay was at the controls, but Janeway was giving the orders.
Whoops...my bad. I see what you did with the spoiler warning there...I thought the second one was about the third example...sorry
[ August 17, 2001: Message edited by: Aban Rune ]