Voyager's continuity in five words:
WHERE IS THE BORG BABY?!?
Add to that...
Where is the Equinox crew?
What happened to the Borg rebellion/Civil War?
Why does Janeway mysteriously forget Kess' warning about the Krenim?
One episode the crew laments the potential loss of the doctor and the fact that he could not be replaced or backed up...the next the doctor has a msterios back up module that is a perfect copy of the EMH.
In an early episode Janeway laments the fact that she does not have any betazoids/telepaths on board...a later episode points out that she DOES in fact have them on board because the have to be hidden.
I'd also add the silly Lindsy Ballard episode to the list. We'll ignore the fact that Harry would not have had a relationship with this woman as suggested since he was still pining for Libby when the show started...there is also the fact that as an episode from late in the series run, it was kind of insulting to have a story about a lost beloved crew member that we NEVER met not heard of in the previous seasons.