Whilst Voyager heads toward the vortex, the Malon apparently disable Voyager's engines; however, when we see the exterior of the ship, both warp and impulse engines are undamaged and functioning normally. Not only that, just before Voyager enters the Vortex, Tom Paris tells the Captain that the engines are damaged and offline; yet, upon exiting the vortex moments later, Captain Janeway orders "Maintain course" even though Voyager has apparently not paused to fix the seriously damaged engines.
When the Voyager is thrown into darkness, you see Tuvok and Kim on the bridge and then the scene cuts to the mess hall as the lights go out. Several scenes later when the Voyager's name is shown, the mess hall is illuminated.
Voyager is 2500 light years from any star system, and all the crew can see through the windows or with sensors is blackness.
It is true that starlight ought to be visible from further away than 2500 light years, and this is why from Earth, other galaxies and distant space objects outside our galaxy are visible to the naked eye or with telescopes. Yet as Seven explains to Chakotay before the opening credits, it is the high concentration of Theta radiation (which they later learn is being pumped in by the Malon) occluding human vision and sensor scans.
It is true that starlight ought to be visible from further away than 2500 light years, and this is why from Earth, other galaxies and distant space objects outside our galaxy are visible to the naked eye or with telescopes. Yet as Seven explains to Chakotay before the opening credits, it is the high concentration of Theta radiation (which they later learn is being pumped in by the Malon) occluding human vision and sensor scans.
Emck said he had to fire 13 spatial charges to drive those ships off. However when counted by how many "pops" are heard/seen onscreen it ranges from 7-12 spatial charges. Clearly he didn't know how many he fired.
The Malon is not interested in Voyagers solution for wasting the dump, the Malon would be out of business. This argument is not logical, when he would use the technology, he would in fact earn more and do less as long as he does not share that technology with other Malon.
When Emck first boards Voyager, he is detained on the transport pad because of the radiation he is leaking. Later in the episode, he walks freely around Engineering with apparently no ill effects to the crew or the ship.
The power goes completely out on Voyager, yet the Holodeck remains operational but with lights out. Regardless of any discussion of whether the matter is either replicated or "photons and force fields," Seven instructs the computer -- which should be offline -- to disengage safety protocols. Seven specifically mentions that "several subsystems are still online," including the holodeck, though this does not explain why the lights are out since the lighting in holodeck simulations is usually part of the program itself.
Earlier in, it is established only the Malon crew knows the vortex location. However later on during the final battle they appear to know where it is with no explanation as to how they found it. One could argue they followed the Malon vessel.