When the cadet takes a holoimage picture of Boothby and Chakotay, Boothby kiddingly tells her not to cut off their heads. We see through the viewfinder's image that she does cut off the top of Chakotay's head, yet later, when the Captain and others review the pictures, we see all of Chakotay's head.
At the meeting with Species 8472, Janeway says they haven't had contact with Starfleet in 4 years. But they first established contact in Message in a Bottle (1998)(#4.14).
If Archer is Species 8472 and they are telepathic, one might expect her to know Chakotay is human by just hearing his thoughts. But the process of converting their DNA to human (or other Federation species) may mute the telepathy, which would potentially be desirable if the trainee infiltrators needed to get good at understanding how humans work without the 'cheat' of reading minds.
Chakotay does not wear Maquis rank insignia. He wears Starfleet provisional insignia with the rank of Provisional Commander. This would not "stick out like a sore thumb" but would instead be acceptable anywhere in the Federation because it is an official Starfleet rank. It's use is generally for civilians who need to temporarily hold military rank. In Chakotay's case, it's because he's not in Starfleet, but Captain Janeway needs him to have the authority of a first-officer while on Voyager. It should be noted that Chakotay was a commissioned Starfleet Officer with a rank of Lt. Commander prior to his defecting to the Maquis.
Tuvok refers to a unit of time (a year) during the negotiation scene. While that unit of time would have no meaning in space and Species 8472 would originally have been unfamiliar with it, the species has been studying Starfleet and would undoubtedly have been arranging their holo-simulation on Earth's 24-hour clock et cetera.
The doctor injects Gentry's human body with something that will revert its DNA back to species 8472. After the change, while the doctor is looking at the head the alien, his line of sight is slightly off and he is not looking right at it. This is because there is no physical prop there for him to focus on. The alien that is seen to viewers is CGI animation.
When Chakotay is in Archers quarters, he picks up a book. The shelf is lit up and the individual books are completely visible, however when the camera cuts back to show Archer and Chakotay the books are not lit up anymore as if there's been no light on them at all.
Chakotay mentions that his last visit to the real Starfleet HQ was on March 3, 2368, in order to resign his commission and fight with the Maquis. The Maquis did not actually come into being until after the formation of the DMZ in 2370, as shown in The Maquis, Part I (1994). Furthermore, Ro Laren in Preemptive Strike (1994) describes a lieutenant commander who was in Advanced Tactical Training with her and resigned to join the Maquis; this was supposedly a reference to Chakotay.
When the admiral is welcoming Tuvok and Neelix to Terrasphere 8, we hear him say 'Starfleet', but his lips don't say the word 'star' before 'fleet'. It looks like he says 'Earth fleet'.
Given the meticulous precision and superior abilities that Species 8472 has demonstrated in the past, it is strange that they neither detected the Delta Flyer in orbit nor immediately recognized Chakotay and Tuvok as being not of their own kind.
Species 8472 can read minds so not only could they have read Chakotay's mind, they would have discovered that the Voyager crew (humans in general for that matter) mean them no harm.
The scene where Chakotay is getting his picture taken with Boothby by the cadet, her rank is circular not rectangular. This gives the viewers insight that it's not really Earth.