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?
Resort + Desi + Riley + Window Cleaner + Witness - S5-E1
Plot hole: Paula Matos comes into her room and surprises Desi and Riley. Paula has a gun. Riley asks her if the gun is ceramic, as no guns are allowed in the hotel past security. It is not answered, but it would be the only way Paula could have a gun. So far so good. But later when they have made a deal, and they are leaving the room, Riley tells Paula to leave the gun behind because there might be metal detectors along the way. If it is indeed ceramic, then there is no need to leave it behind. And if it is metal, how did it get past the metal detectors in the first place? One or the other premise is wrong. (00:24:05 - 00:26:00)
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.