How does Natalia get from the baggage compartment to the cockpit?
The plane that they were in is an Airbus A300-B2 which has a seal-tight cockpit door, it should have been able to keep the bees out but didn't, which could mean that it was open during the incident. It still doesn't explain how she managed to dodge the bees through the cabin, which she would have had to traverse in order to reach the cockpit. It's possible that, unlike real bees, these magic ghoul ones are slow and you can easily dodge them if you knew where they were. Or maybe, she's just got crazy skills.

The Manga doesn't shed any light on how she got through the cabin, though the original light novels may.