#401 Scorpion... Voyager towed at transwarp speeds by the Borg who would have noticed tugging additional weight and Voyager also leaves the Universe. It's unlikely that the Scientists cloak would have worked flawlessly in Fluidic space if they had never seen fluidic space before.
#402 The Gift... Kes was melting the ship. If they were experimenting on her, they would have stopped what they were doing to her as she was a danger to their ships moored to Voyagers hull. Plus Kes now had super telepathy and would have noticed them walking about, and the leap of ten thousand light years would have been fucked up if Voyager weighed three times as much as it should of when kes was intuitiving how to fling them Earthward... If three scientist ships were moored to the hull, they would now be 10 years from home minimum and fucked. Also that might mean if those ships where not stuck to the hull Kes would have thrown Voyager 30 thousand light years and not just 10.
#403 Day of Honor... Voyager was raped by Space Pirates. Took it's core. This again would have been call for the aliens attached to Voyagers hull to cut their losses if this ship no longer had a viable life support system for their experiments.
#404 Nemesis... These aliens would not accept the competition of another group of mad scientists experimenting on their experiments as it would ruin their controls and actives, unless this was them? they weren't obviously but with forethought behind the scenes from the producers it would have been a good fit for a little foreshadowing.
#405 Revulsion... Janeway promoted Tuvok despite what happened in Prime Factors. Some invisible alien scientist had obviously slipped heroin into her coffee.
#406 The Raven... Voyager invaded alien territory against the express instructions of a powerful militant defensive force to get Seven back from her vision quest. How sure were the Scientists really about their cloak that they would let Voyager drag their species into a war too? But the dreams causing Anika to follow the signal from the Raven could definitely be the Scientists experimenting on Sevens brain making it more attuned and receptive.
#407 Scientific Method... Zero hour.