Stupidity: When Jonas says he saw a creature go through the walls, people want to assume he must be hallucinating. Yes they sweep the base, but Carter questions its ability to pass through solid matter as if she's never seen that happen. When Jonas sees a creature again on the device with Carter there, she gives a look like he's going crazy rather than at least try to use a TER to scan for it. Plot wise it seems this is done just so O'Neill can leave the base and spread the "infection."
Stupidity: Some ancient advanced civilization took to the task of building this amazing net of stargates that enables instantaneous traveling over hundreds of light years or more, but any stargate can be disabled by anybody just by covering it with dirt or rocks. Apparently if the stargate is buried then it becomes inactive. See Season 1 EP.1.
Suggested correction: This is just you having a different opinion on how the Stargates should work. In fact, the ability to make a Stargate inactive by burying it is a brilliant move by the Ancients. Burying the gate, or even creating a barrier, prevents enemies (like the Goa'uld) from having a convenient way of invading a planet. Although some races, like The Nox, show the ability to activate a Stargate without having to form an unstable vortex.