When Voyager is attacked by the Bothan, Janeway calls for Kes to join her on the bridge, and Kes acknowledges with "Right away." However, Kes never shows up; in fact, she never even leaves sickbay, as can be seen later. Although Janeway was influenced by the Bothan at the time of her call, she was not yet fully delusional, and nothing indicates that her communication with Kes was not genuine.
The goof items below may give away important plot points.
Near the end, when Janeway gets in the turbolift to go from the Bridge to Engineering, she looks over and sees Chakotay in the catatonic state, but when the turbolift doors open, she is the only one inside. While the figure of Mark is understood to be her hallucination, there's no indication Chakotay was, as well.
At the end of the show Captain Janeway says that they cannot be certain that the alien was ever even on the ship. Although people were hallucinating, and while under that influence they could be feed incorrect information from the ships computer as part of that hallucination, telepathy does not affect technology so once everyone was no longer under the influence of the alien a quick check of the ships internal sensor logs should have shown if there had been an alien intruder or not.