When Sklar gets pushed out of the mag-lev carriage and falls through the clouds, his body vanishes just before he falls out of shot.
Neelix accelerates the mag-lev carriage to 47 kilometers per hour, starting from the planet's surface. Within a couple of minutes, Tuvok states that they are 30 kilometers above the surface. It would take almost 40 minutes to get that high at 47 kph IF they were starting on the ground, which they're not. The mag-lev had already been climbing for an unknown amount of time, presumably an hour since before Neelix raised the velocity he stated they were at 30 kph. This would make Tulok's statement completely logical.
The roof hatch of the mag-lev carriage is opened twice in the upper atmosphere. All air should be blown out, but the characters are not pushed out of the vessel and continue to breathe without difficulty; however, when the main hatch opens a little later (while the carriage is still at the same position), the blow-out effect becomes moderately apparent. Despite being low on oxygen reserves from the beginning, nobody seems to suffer from oxygen deprivation even then. Of course, that comment is based on EARTH's atmosphere and this is an ALIEN world with an unknown atmospheric height.
Starfleet transporters have always been tuned to the shield harmonics so people and objects could be beamed aboard or away with the shields up; therefore, Tuvok, Neelix, and the two Nezu with them being beamed aboard during a battle is not a goof.
Voyager is able to track the asteroids as they move on a set path up to six hours away. At no time do they try to move to the asteroid's position and destroy it long before it would strike the planet. For some reason they keep waiting for the asteroid to reach the planet before trying to destroy it.