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: When Lindsay brings Tru breakfast in bed on the second version of the day, she is excited that Tru remembered her birthday, and she also mentions that nobody else did. But it's still very early in the morning. It's not at all reasonable to assume that anybody forgot her birthday just because they didn't call before 8am.
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.
Plot hole: There is never any explanation of how the MPs find Jake at Bridget's house. He had apparently been at her old house for hours (if he went there directly from the hospital) without the MPs finding him there, so they must not have been following him. Tru managed to find out her new address, and somehow the MPs found him there, even though they didn't know anything about Jake's relationship with Bridget.
Plot hole: Meredith is subjected to a random drug test at work. However, the drug test is announced late at night. Tru is already working her "graveyard shift" at the morgue, so we know the regular workday is over. Hardly anyone would be in the office. Therefore, it doesn't make sense for the company to be administering this drug test, said to be requisite for all employees, at that time.
Plot hole: Justin is a police officer. As a result, his actions at the end of the day the first time it plays through make no sense at all. His girlfriend tell him that she has shot Nicole, and that the crime will be pinned on him because she used his gun. But he knows that there will be no gunshot residue on his hands, and there will be on hers. He knows that his whereabouts were accounted for at the time of the murder, because he was at the diner in full sight of any number of people. He knows that there is not a single shred of evidence aside from the gun, which has his girlfriend's fingerprints all over it anyway. If he were to simply arrest her now, there's no way she wouldn't be the one to go down, rightly, for the crime. Instead, he decides to tamper with the corpse and shoot two bystanders, in order to protect his innocence. It makes no sense at all.
Plot hole: Meredith submits to the drug test at her office. In the next scene, which takes place later the same evening, Harrison tells Tru that Meredith's test came back positive and she was immediately fired. But it takes at least 24 hours to get a result from a urine test at all. If the test is positive, the sample must be subjected to a more thorough examination. It usually takes at least 72 hours to get the results in that case. There's no way Meredith's positive results could have come back in less than six hours, even if a lab had been open late in the evening.
Plot hole: Harrison and Lindsay hooking up was pretty much a given, based on the course that events took in the episode. But why were they doing it in Tru's apartment? Harrison and Lindsay each have their own apartment, so the only reason for them to be on Tru's couch is for entertainment value.
Plot hole: John is slightly surprised to find that Tru is acting as bartender for the party, but doesn't dwell on it any further once she explains that she was supplied gratis to make up for the earlier "problems" with the room. But John should actually be extremely alarmed to find her there, given that he poisoned the ice and expects the other guests to drop dead. He certainly wouldn't want any witnesses to that.
Plot hole: Tru and Lindsay are making all their plans for the reunion on the day of the event, including whether or not they will attend and whether or not they will bring dates. But a high school reunion requires an RSVP in advance, just like a wedding or bar mitzvah. So they should have had to figure out their plans weeks earlier.
Plot hole: Why did Tru have the reunion invitation on her desk the morning of the event? It seems as if she had received it that day, since Davis asks if she's going and she says no and throws it away. That's something you'd do with the invitation upon receiving it and deciding not to go. But it doesn't make sense for the invitation to have gone out the day of the party.
Plot hole: How did lily pollen get on Nicole's dress? Justin's girlfriend never touched Nicole; we saw the confrontation the first day, and Nicole just shot her and then must have left very quickly because nobody saw her. Even if Justin's girlfriend were covered in the stuff, it couldn't have somehow jumped onto Nicole.
Plot hole: When Marco brings Andrew's corpse to the morgue the first time the evening happens, he says that Andrew was died "in his ex-wife's house." However, during the second instance of the day, it is eventually revealed that Sarah is actually still married to Andrew, and they are just separated. Sarah may have lied to Harrison about that, but the police would have gotten accurate information. In fact, when Sarah calls the police (the second time), she refers to Andrew as "her husband."
Plot hole: When Tru first arrives at the military hospital, a security guard tells her where Jake's room is, and she proceeds in that direction. Then a nurse tells her that visiting hours aren't until noon, and it's only about 9:30am. But surely the security guard would know when visiting hours are, so why wouldn't he mention that to Tru when it's obvious that she intends to visit a patient?
Plot hole: At the end of the episode, Lindsay says that her note made one man a liar and another man gay. But how does she know that Craig lied? The first time, Craig said that he didn't get the note, and also demonstrated that he had no idea who Lindsay even was. The second time, Tru intercepted Craig and asked him to be nice to Lindsay. So he again told her that he didn't get the note, but also said that it's a shame he didn't get it, because she's really amazing, but it's too bad because now he's married. So he barely lied to Lindsay, and she would have no way to know about it. Tru didn't hear what Craig said, so she wouldn't know if he lied, either, and even if she did she wouldn't tell Lindsay, because the whole point was to make her feel better about the situation.
Plot hole: There's too much bruising on Paige's arm in the original timeline, given that she only had one injection given to her by a med student (on the day of her death). She doesn't appear to have had any previous injections when Tru looks at her arm in the second timeline
Plot hole: Richard tells Tru that Carl periodically comes around threatening to exact revenge on him unless he pays him off. The audience eventually finds out that Richard hired Carl to kill his first wife, so it makes sense that Carl can demand money from Richard and not face any consequences. But why does the story make sense to Tru? The way Richard told it, Carl has nothing on him, so there's no reason for him to be paying him off. Tru should ask her father why he doesn't simply get a restraining order.