Plot hole: They only take out the shrapnel from the gut shot - they never deal with the shrapnel in his shoulder at all. (00:04:25 - 00:05:00)
Plot hole: Gracey loses the Dean while she's sleeping, but Ms Loon is revealed later to have taken the Dean, so how did she get into the room?
Chapter Seven: The Massacre at Hawkins Lab - S4-E7
Plot hole: The upside down should be mirrored, i.e. all left is right and right is left. When the team finds a gateway where Chrissy died, they should be seeing a mirror image through the ceiling. Also, all buildings should have been reversed. Directions to get there on the bike would have been confusing and reversed, and when any writing was seen in the upside down, it would have been backward.
Lidar + Rogues + Duty - S3-E16
Plot hole: Riley's father Ellwood shows up unannounced at Phoenix headquarters. The address for the Phoenix Foundation Headquarters is classified, as is Riley's job. How did he know where to go? (00:22:10)