After the first time the photonic energy mass breached there was supposed to be a second one there however only one is shown. It's not possible for them to have not had the other container empty during the experiments they'd conducted on the life forms. Considering they gave the Doctor the other life form for the holodeck to release to Grendel.
When the doctor walks with Freya in the forest, she shows him a powerful plant. The doctor, who has encyclopedic knowledge, identifies the plant as a fungus called Amanita Muscaria and says it is poisonous. If the writers had chosen any other mushroom, this would be an obscure goof noticed only by mycologists or other mycophiles, but the Amanita Muscaria is the most readily and broadly identified mushroom in the world - the big red one with the white dots. What is shown is a handful of white flimsy mushrooms, perhaps the edible oyster mushrooms or white chantrelles.
When Freya first confronts The Doctor, he already knows her name and rank from reading the Beowulf saga - but Freya is nowhere mentioned in the saga. Around line 2022, there is one, and only one, mention of the king's daughter, Freawauv, who serves the warriors wine, giving no clue as to her age or to having any military (or other) authority.
At one point Tuvok speculates that Harry Kim could have undergone matter-energy conversion. This would, of course, mean there would be nothing left of Harry to find, but it would also mean there would be nothing left of Voyager either.
If you convert a human body (60-70 kilograms) to energy you would get an explosion very much larger than the largest nuclear bombs ever detonated.
For comparison "Little Boy" converted just 1/8 of one gram into energy.
The swords used on the holodeck are not exactly appropriate for the Viking time period, being post-Norman swords of the early Middle Ages rather than the type of short stabbing weapons that were prevalent in Norse culture of the sixth to eighth centuries.