The Delta Flyer fires four, not three, photonic missiles at the Malon vessel. One missile completely misses the targeted vessel and flies right past it. Seven of Nine calls out "Three direct hits." Seven is in fact correct.
B'Elanna reacts badly over the "news" Chakotay gave her about their Maquis friends being killed. Though the news arrived back in Message in a Bottle (1998), it only now adversely affects B'Elanna, shutting her down emotionally from everything around her. This is a reaction that has developed over time, not immediately from some presumed recent news.
Neelix never heard of banana pancakes before yet knows that pancakes are ordered by the "stack." The stress is on the word "banana." It's likely he's heard of pancakes before, just not from a recipe that involved bananas.
Janeway orders Chakotay aboard the Delta Flyer's maiden voyage. Shortly after, Chakotay returns to the bridge with no questions asked about why he's not aboard the flyer. Janeway and Chakotay merely exchange knowing smiles.
In the Next Generation season 6 ep. "Descent" Data asks LaForge for a second voice command in order to delete the holodeck safety protocol's. However, B'Elanna Torres can disable them by herself at will.
Chakotay orders the holodeck doors sealed, but does not order the computer to unseal them before he leaves.
Lieutenant Torres says she was kicked out of Starfleet at the age of 19. This age may be considered accurate however her being kicked out isn't correct. She dropped out of Starfleet as she has mentioned it many times. Even when Captain Janeway interviewed her for Chief Engineer she said she dropped out/quit the academy.
When Lieutenant Torres was talking about her father she said she was 6 when he walked out on her. However in season 7's "Lineage" the flashbacks show her to be much older than 6. She was around 12 at the time when he walked out on her.