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)
Left Behind - S1-E9
Plot hole: It's revealed that Chronos is Mick from the future after he was abandoned by Snart. However, in the episode White Knights (episode 4) the earlier version was able to sneak up on Chronos and surprise him with an attack from behind. If that was a future version of Mick then surely he would have remembered the attack coming and could not have been so easily caught off guard.
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?
Seeds + Permafrost + Feather - S3-E17
Plot hole: The team is trying to recreate the movements of a murdered seed vault employee by using his phone's geolocation attributes (compass, accelerometer, altimeter, etc). They are trying to backtrack from the place they found the murdered employee to where he first surprised his killer. They backtrack using the data from the employee's phone, and there is another set of data shown on the computer. But they only have one phone's data to work with. Where did the data presumably from the killer's phone come from? (00:12:50)
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.