At the beginning of the episode, Seven finds the weapon while Voyager is in dry-dock but it is “out of phase” and she indicates that they have found where the weapon was placed but not when.
At first I thought this implies that the weapon was placed before that point (given my linear experience of time) but they later conclude that the weapon was placed two years later during an attack by the Kazon.
Given it’s a time weapon, it might make sense that the weapon exists outside of time and can be seen prior to it being placed (in a linear sense), but when Seven jumps forward to two years later and goes to the same hatch during the Kazon attack, she can’t see the weapon because it hasn’t been placed yet. So this implies the weapon does follow the normal rules of linear time.
So if she can’t see it at that point, how could she have seen it while Voyager was in dry-dock two years previously?
See this timeline for clarification:
Dry dock Kazon attack Seven (Can see) (Can’t see) from here |_______________|______________| Time -> | Weapon Placed
Note: I’m willing to accept this is just a plot hole given that, as enjoyable as this episode was, it was badly written in a couple of places (Janeway recognising the time ship as Relativity without being told, and Janeway knowing Seven was from three years in the future, again without being told).