Learn Spanish (Latin America): Perdí el vuelo porque no había pasado la seguridad. - I missed the flight because I had not passed security.

We use the past perfect (había pasado) to show that one past action happened before another. You missed the flight (perdí) in the past, but failing to get through security happened even further back in time. Using había pasado (had passed) makes this timeline perfectly clear.

Doesn't perdí come from perder, which means "to lose"? Why is it translated as "missed"?

You are exactly right that perder usually means "to lose." However, it is also the standard verb for missing a flight, train, or bus. Just remember: if you are missing a person emotionally, you use extrañar, but if you miss a mode of transportation, you use perder.

Could I put the no between the two verbs and say había no pasado?

No, in Spanish you can never separate the two parts of a compound tense. The conjugated form of haber (había) and the past participle (pasado) act as a single unit. Negative words like no, as well as any object pronouns, must always go directly before the conjugated form of haber.