The Would-Be Prince of Darkness - S1-E3
Plot hole: During the credits, Chloe said of the victim "coroner puts her time of death between 1 and 3am", and she does indeed ask Ty's obsessive fan / ex-gf where has she been during that timeframe. When she looks at the security tape, the timecode starts rolling at 22:18 and goes on "for 3 hours." That does not account for the time of the murder at all, she has no alibi for the second half of the suspected timeframe! Not to mention, she said she saw Ty kiss the victim. When could she possibly have seen that? It's unlikely that before 10pm Ty was already drunk and getting randy with the girl, with the house full of guests. (00:25:00)
Plot hole: There is a rather confusing revelation when Chloe is shown the recording Joe Fields made for his daughter to see in the event that he were to die. In the recording, Fields tells his daughter that he did not kill the cop (Chloe's father). Chloe then notices that this is true because based on the timestamp on a sign in the background of the recording, he made the video 3 minutes before her father was killed. But this would be impossible because at that point the cop in question was still alive.
Suggested correction: That was the whole point of the episode. Joe Fields never killed Chloe's dad (officer Decker). Fields was innocent and took the fall for his murder. The time on the sign showed that Fields was too far away to have killed her dad. Her dad was in fact assassinated (arranged by Perry Smith) and not killed in a robbery attempt as previously believed.
But why would he even make a tape saying he didn't kill the cop if it hadn't even happened yet? Makes no sense. Did he go back in time?
I think you should rewatch the episode. He already agreed to take the fall for the murder. He knew the murder was going to happen. He made the tape for his daughter before he went to prison (and possibly made it before the murder as to further prove his innocent). The tape was to be given to his daughter after he died so that it wouldn't affect the deal he made.
They never made the connection that he knew the murder was going to happen, instead they went on a wild goose chase instead of going bit by bit.
But then as Bishop is saying, Joe Fields knew that the hit was going to go down. He made the video declaring his innocence so his daughter would eventually get the tape. Whether he knew that he would be exonerated is another matter. But the point remains the same. He knew that the cop was going to be killed and simply prepared for it. No mistake.
The Would-Be Prince of Darkness - S1-E3
Plot hole: Lucifer is not wearing a wire, since the 'fixer' could get suspicious. In the next scene, Dan, who is the person that Lucifer should introduce, is in constant contact with Chloe for no urgent reason. Why would the fixer not check him for a wire too?
Plot hole: Lucifer's evil brother Michael appears too Dan as he is praying upon Charlotte's grave from heaven. He tells Dan he can right all of his wrongs. His plan is to hurt Lucifer. It's stated that God sees all and hears all. "The eyes of the Lord are everywhere, keeping watch on the wicked and the good" (Proverbs 15:3). Doesn't make sense how Michael is able to travel from the Silver City to Earth to hurt Lucifer without Dad knowing or having any input, since Michael has a direct line to his Dad. (00:17:00 - 00:19:40)
Sympathy for the Goddess - S2-E17
Plot hole: Charlotte tells Chloe that she was talking to the man on the phone when she hears gunshots. Being a veteran detective Chloe should have noticed since the man's gun was in his pocket (Chloe comments that his phone was found on him) that he couldn't have been using it when he was shot, therefore Charlotte was lying. Yet she never realised this.
Plot hole: Lucifer and Amenadiel realise baby Charlie calms down and gets put to sleep when he sees Lucifer's devil face. Dan just left Amenadiel's house, and he gets a phone call with Lucifer's voice telling him to come back to the house. He turns around and sees through the window Lucifer's devil face. It is revealed that Lucifer's evil twin brother called Dan to expose Lucifer. Makes no sense how Michael knew that Charlie responds to Lucifer in that way. He would've been seen peeking through a window. (00:49:35 - 00:52:00)
Suggested correction: You essentially explained the plot. Michael had been watching them the whole time. In fact, when Michael calls Dan, Dan first responds with "hey, man, what's up?" because he saw that it was Lucifer calling him. One way for Michael to have Lucifer's phone is because he saw Lucifer throw it out the window earlier.