Plot hole: One of the flying dragons impacts the right outer engine of the B-29, and the fire spreads to the right inner engine. The crew lands the plane on the island, and the girls rebuild both engines, despite the fact there are no parts available on the island.
Plot hole: In the scene where Ba'al goes through the stargate and arrives in 1939, the event horizon from the stargate puts a hole in the haul of the ship. Later when SG1 goes through the stargate the hole is covered with ice. The event horizon created from SG1 would have been the same as the previous one and removed the ice from the hole.
Plot hole: We don't see any herbivores in the underground world - just fish and little birds. A T-Rex would need lots of big game to survive.
Plot hole: Rhona Mitra is told she can't fly into Scotland because it's a "no fly zone." But it's all part of the UK, and she's being sent in as part of a UK government operation. The only group enforcing the no fly zone would be the UK government, so they could send her in via whatever means they like.