Neelix brings some food to Gar who is in prison interrogated by Tuvok.
The food is poisoned, and can be seen as torture. Torture is strictly forbidden by the Seldonis IV Convention treaty.
When Chellick restricts The Doctor to Level Blue, the Allocator transfers The Doctor around Level Blue as if Level Blue had holo emitters, but in fact the Allocator uses transport technology to move the Doctor's holotransmitter (and thus The Doctor) from place to place.
Neelix comments on Tuvok's threat of a forced mind meld, but Neelix had not yet entered the room when Tuvok said that. But the ruse may have been planned in advance.
When Voyager arrives at the "asteroid" after they cross referenced their sensor logs and long-range scans for the iridium, the "asteroid" looks like a planet. Specifically, the planet where the Delta Flyer crash landed in season 5's "Once Upon a Time". If it were an asteroid it would be much more geometrically uneven.
When the Doctor, Tebbis, and Voje were injecting the cytoblobin in the patients who had the chromo viral infection, it can be seen that Tebbis did not grab another injector after he injected the first patient. Clearly it wouldn't have injected cytoglobin in the next patient he treated when the injector was only used for one patient. He should have grabbed another injector in the case the Doctor carried around.
When Voyager arrives at the planet where the Doctor is Janeway does not attempt to hail the Doctor. Instead, she hails the ship and sends B'Elanna and Chakotay down to the ship to get the Doctor. Instead of doing all that the simplest thing she could have done is hailed the Doctor, had him access the main computer to have his holo matrix no longer interfaced with the main computer therefore Voyager could have just transported him back to the ship that way.
When the doctor talks about his plan to escape Level Blue, although a nurse sits at a desk nearby well within earshot she may have simply not heard him or maybe even willfully ignored him because she was not loyal to the allocator.