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)
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.