Plot hole: Huge plot error: Apophis and Clorell (Skara) should not have survived the explosion in Season 2, Episode 1 (when they attack Earth with two ships). In "Family" they explain that Apophis and Clorell survived by escaping through the stargate aboard Clorell's ship moments after Daniel Jackson did the same. However, when Daniel Jackson escapes through it, Apophis and Clorell are not even on the right ship, and there is 1 second left on the C4 timer when Daniel escapes. They actually show Daniel Jackson escape, and then cut to Apophis and Clorell still aboard their ship. So apparently, Apophis was able to "ring" from his ship over to Clorell's ship, make it to the stargate room, dial an address, and escape through the stargate all within literally 1 second. Is this guy related to The Flash?
Suggested correction: That's not what happened or what was said. Daniel suggested Apophis and Klorel used the rings after he did, not that they used the Stargate after him. In "The Serpent's Lair", we see Apophis and Klorel use the rings BEFORE Daniel uses the Stargate. But we don't actually know how much time is meant to be left on the C-4 when they use the rings. They ended up using the Stargate before Daniel did and they never cut to them on board after Daniel escapes.
Shift Into Turbo: Part I - S1-E1
Plot hole: Divatox and co. live in a submarine in Angel Grove lake. In "Hogday Afternoon", Angel Grove lake was drained to about 30ft at the deepest. The lake would have to be several hundred feet deep for a large submarine to hide there.
Hiren Lake Legend Murder Case: File 3 - S1-E6
Plot hole: Kindaichi's denouement can happen only because the killer misses half a dozen people leaving the cottage covertly; Kindaichi does not have a clue of the killer's observation point, and despite what the detective says, the killer was not just listening, but watching them too with binoculars. Moreover, moving a microphone sensitive enough to capture the sounds of the whole room would produce noises which would have alerted the killer that they were tampering with it.
Plot hole: During Ryder's report, as Bruce and company watch it on TV, the camera suddenly zooms in on Joker standing on a catwalk above Ryder, and none of the crew, especially not the camera man who caught the villain, makes a comment about this. They may have thought the Joker (or rather an impersonator) was perhaps a surprise gag in the show, but since this is supposed to be a serious documentary report, it is still strange that they wouldn't point it out.