Plot hole: Throughout the series, auxiliary characters are always far too willing to give all kinds of information to Tru. Doctors and registrars constantly give her privileged information about patients and students. Tru is often able to retrieve information like addresses and phone numbers from people's service and utility companies, when normally you must verify your own information before they will even talk to you about your account. Of course there can't be an episode if Tru doesn't quickly find the person who asked for her help, even though she doesn't usually know much more than their name, but it's still a bit conspicuous.
Plot hole: Gardez and Michelle Carey both disappear with no explanation. While Gardez's disappearance benefits the plot, in order to introduce Jack, there's never any mention of why he's gone, be it personal/medical leave, reassignment, etc. Ditto Michelle: she was so determined to learn the truth about Tru, so her disappearance doesn't make sense.