Plot hole: In episodes where Sam and Dean are required to perform spells/rituals at certain times, the issue not quite seen is that not all clocks are exactly in sync with each other, meaning that the clock they are using could be off by a few minutes especially if dealing with different time zones or time periods. (S07E12, Time After Time).
Factual error: When the doctor says that the dead man has a high lymphocyte percentage indicating a viral infection after she looks down the microscope: 1) What they show in the microscope looks nothing like what is actually visible down a light microscope (especially the supposed lymphocytes) and 2) Even if she could see what they showed, it wouldn't actually indicate that the infection was viral.
Mannequin 3: The Reckoning - S6-E14
Continuity mistake: When the guys tip Rose into the grave, her eyes are open, but as she lands and dirt falls over her face, her eyes are closed. A dead person's eyes don't close on their own. (00:25:20)
Bloody Mary - S1-E5
Continuity mistake: In the scene where Jill is looking at her 'Bloody Mary' reflection, the lines of blood coming from her eyes go down and straight over her mouth (because she hasn't smeared them like the real Jill has). But as she begins to talk, the lines switch from being over her mouth to off to either side of her mouth and back multiple times. (00:14:20)
Hell House - S1-E17
Visible crew/equipment: Right before they light the house on fire, the shot cuts the to the hell hound guys and a cameraman is running up to them on the right. Not just an arm - his whole body, including the camera.
Continuity mistake: In the opening scenes, Vamps drags Chrissy Chambers through the shattered passenger-side window of their crappy vehicle, but by Sam and Dean's arrival, that window is magically unbroken. (00:02:30 - 00:15:55)
Continuity mistake: When Sam and Dean break into Lori's dorm, Sam notices (and the camera pans towards) an open window. The camera then cuts to Dean. When the camera cuts back to Sam the window is closed. We watch Sam open the window and climb through it.
Mannequin 3: The Reckoning - S6-E14
Audio problem: In 6.14 "Mannequins 3: The Reckoning", when Dean goes up to talk to Ben, Ben is playing a video game. Dean says something along the lines of "There's no way plants could kill zombies", therefore pointing out that Ben is playing Plants vs. Zombies, but the sounds coming from Ben's gaming system are not from Plants vs. Zombies.
All Hell Breaks Loose: Part 1 - S2-E21
Factual error: Dean finds a body in the house that burned down. The arm has a metal watch still on the wrist with hardly any damage. It has some black soot on it but that's it.
Suggested correction: Your entry is based on opinion/theory only. It's possible for someone who died in a fire to have parts of their body to not be affected by the fire.
Factual error: At the beginning of this episode, it says "one week later", then it shows Dean and Sam go to the victim's apartment. The blood is still bright red. After a week it would be darker.
What Is and What Should Never Be - S2-E20
Audio problem: Dean is in the cemetery talking to his father's grave, trying to figure out what's happening to him. In a continuous shot, right after Dean says "like it doesn't want me to be happy", you hear him say, "of course I know what you'd say" but his mouth doesn't move at all. (00:23:00)
Continuity mistake: In the very first scene with Lori and Rich kissing in Rich's car, Lori's seatbelt is shown to be over her arm close to her shoulder. The camera cuts to Rich and back and the seatbelt is now behind her arm and lower without her having moved at all.
Continuity mistake: When Sam approaches Pamela to give her a hug, you see his hand on her arm. In the next shot he is still walking towards to her and his arm is hanging at his side.
Taxi Driver - S8-E19
Continuity mistake: When Crowley comes to the ship and finds Kevin Tran he blew out the glass on the ship to get rid of the sigils. When Sam and Dean get to the ship to check on Kevin, and they notice he's gone, all the glass isn't broken and the sigils are still there.
Bloody Mary - S1-E5
Continuity mistake: When Sam is looking at the mirrors with night vision, we see him pause and say to Dean "Look at this." The camera then cuts to an extreme closeup of the camcorder screen and the image on the screen is different to what was on there before. (00:18:15)
Continuity mistake: At the start as we see the victim on the plane, we see a blonde woman sat in the middle seat 2 rows in front of his row. When he gets up to stretch his legs, this blonde woman has now changed to a Chinese one. (00:02:45)
Audio problem: The pilot asks Amanda how she is at the start. When Amanda replies the audio doesn't match her mouth. (00:02:10)
Continuity mistake: Dean circles the newspaper article on Sophia Carlton. When he hands it to Sam the circle is different. (00:03:20)