GM Intrusions take a while to grok, but once you "get it", you'll see they're actually a great tool to grease the narrative wheels.
The One Rule that Lets You Break All The Rules
The way I see it, as informed by the book, and by various blog posts, GM Intrusions are a way to break the rules within the framework of the rules. With them you can handle everything from a PC getting their weapon stuck in an enemy's carapace, to just happening to be standing on the wrong place at the wrong time as a trap-door opens. As the blog post I link to at the bottom states, it would be pretty weird for the GM to just tell you that your gun jams, unless your system has specific mechanics for guns jamming. Rather than provide specific mechanics for gun jams, and every other type of problem that could conceivably arise, GM Intrusions give you a way of creating problems that the rules don't cover, without breaking immersion.
Where I think you may be going wrong is in thinking that Intrusions are just an extra bit of narration. In actuality, they are a special kind of narration, in which, through bad luck, something complicates the character's life. I would almost always treat a GM Intrusion as bad luck rather than incompetence (because PCs shouldn't look like jackasses).
They are a mechanical way to open up a dialogue between the GM and the player, as facilitated by offering and rejecting points. With this back and forth, you create what is acceptable and desirable within the fiction you are creating together. The GM offers 2XP as a carrot to accept a problematic twist. The player either accepts this, implicitly stating that this kind of thing is OK in the game, at least in this instance, as well as receiving an opportunity to reward a fellow player for whatever behavior they think is worth rewarding. Or, the player spends his hard-earned XP to say, "No, I don't like that, at least not this time".
Please review this blog post on the Alexandrian for further details