You get experience points based on your score for the mission. (Scoring missions is explained in the handbook from the basic set.)

Difficulty level of common threats: 1 for white-symboled, 2 for yellow-symboled, 1+2 for both mixed together.
Difficulty level of serious threats: 1 for white-symboled, 2 for yellow-symboled, 1+2 for both mixed together.

Order of difficulty: {nastiest} RED > YELLOW+RED > (YELLOW == WHITE+YELLOW+RED) > WHITE+YELLOW > WHITE {easiest}

This game's been out for about a year now, so I must've missed something from the rule book, but here goes..

I'm aware of the mission points to experience points conversion, that's easy:
2 + round_down(missionPoints / 10)

But what about Mission Points? The rulebook tells us this:

And here's the basic set's handbook:

This clearly contradicts with the information on "Threat difficulty"

Shouldn't YELLOW yield more points than WHITE+YELLOW?
And what about RED threats?

Any help is appreciated

The mission difficulty is already included when you create the threat decks. The points that you have to gain when calculating your score are printed on the threat cards.

I advise you to re-read the basic game's manual in order to understand how the scoring works because it seems that you are using the mission difficulty symbols as multipliers which is totally wrong.

Hey, thank you a lot! Now to break the news for my group, and subtract an XP point or two (luckily we're still between levels 1 and 3).