Stupidity: The eco-terrorists leave the Orca completely unattended allowing Madison to take it without anyone realizing until she is long gone. In addition, they don't post any guards at the exit of the bunker and Madison simply walks away without anyone noticing her at all.
Suggested correction: They leave the Orca in their empty command room within a bunker filled with loyal men. There is no way anyone could have broken in and stolen it. Madison had the advantage of already being in the bunker and even then had to navigate through the air ducts in order to steal the Orca and escape. They wouldn't have armed men visible immediately outside because they didn't want anyone to notice that they were there.
Either one of these issues by themselves wouldn't be particularly stupid but the combination of them both would indeed allow someone to just walk in and take the Orca. You don't need to post a visible guard at the exit, but nobody is watching the exit at all.