It's stated that a shuttlecraft is left behind with Janeway and Chakotay when Voyager leaves the planet; however, at the end, they simply beam up with no mention of it.
When Chakotay is taking the three gray and beige pieces out of the shipping unit, he takes the third one out twice. This is noticeable when the camera angle changes on the third piece.
By beaming away from the planet without retrieving any of their equipment, Janeway breaks the Prime Directive, as leaving technology lying around for any visiting aliens to come upon could change the course of alien development and tip the balance of power in that region.
But, Janeway and Chakotay packed all the equipment up and stacked it outside the shelter suggesting the rest was beamed separately back to a cargo hold, and the only thing left behind is the empty shelter, which doesn't have any unknown technology and therefore would not break the prime directive.
When Janeway gives Tuvok command of Voyager, his new rank is obviously Captain and he is addressed as such; however, his uniform still shows his rank as Commander while Janeway and Chakotay remain on the planet. However, the commanding officer of a vessel is always referred to as Captain, regardless of actual rank. Further, at this point there is no one available to promote Tuvok to Captain (or any other rank).
When the storm hits, it is unclear why Janeway and Chakotay do not take refuge in the shuttlecraft that was left for them.
The conversations about the Vidiians center on the risk to Voyager of contacting them for help with the virus, as the Vidiians could set a trap. Yet the risk is also to Janeway and Chakotay, because if the Vidiians know the virus and the planet, they will go there knowing the stranded crew are sitting ducks.