The list is long -- though the love is deep!
Regarding your first issue: never mind that the Robinsons' vast "junkyard in space", pardon the expression, seemed magically to regenerate after they left Priplanus (or what was left of it) at the end of Season 1 -- how did they cram all that stuff into the Jupiter 2 in the FIRST place?!? As for the Space Pod, perhaps we can simplify matters by assuming it just didn't exist in Season 1 (no, don't ask me how!), since not only did we never see it then, but surely Professor Robinson would have used it for his scouting mission ("Island in the Sky") in preference to those pathetic parajets. And as for the Chariot, I've always been stuck by how quickly its assembly seems to have been accomplished (it must have been fast, because they needed to begin searching for John ASAP) and the absence of tread tracks around it when the first drive off -- talk about modular!
Now to your second point, concerning the Jupiter 2's multiple levels. As I commented a while back in this forum, although the viewer could be forgiven for concluding that the J-2 must work something like Dr. Who's TARDIS, opening up into other dimensions, a spacemodeler named Jon Rogers has evidently figured out how to reconcile all three levels in normal Euclidean space! See "The Saucer Fleet" by Jack Hagerty & Jon Rogers (CG Publishing, 2009) for the amazing details.
Of course this only scratches the surface of all the glitches in LiS, but I like to think that enumerating them all actually enhances one's enjoyment of the series. works that way for me, anyhow.
See 3 other replies