Firstly the Skirmish rules say that you only get one attack. If that is the case, why do some character cards give models to attack twice? I did wonder if it due to those cards also being used in the Campaign, but given that there are smaller card versions for the main characters I couldn't see that as being correct, am I missing something?

From the Skirmish guide:

Attacking: Figures can only use one of their actions to attack per activation. This includes using special actions that involve performing one or more attacks (such as the Nexu's 'Pounce' or Darth Vader's 'Brutality').

In the mission with the 4 counters on the shuttle (sorry don't have the details to hand) if refers to flipping them, but gives no more information. Are they supposed to start face down (greyside up)? Do they all have to be the same colour? It's a bit vague (unless I'm missing something here)

Like most games, there are models that override the basic rules, which is what these do with characters and order special rules.

What mission is it?

Sorry but that still doesn't make sense. As you see in the Skirmish rule snippet it rules out Vader's Brutality and Vader is a character. Or am I still missing something here?

Sorry about the skirmish name as well. Played it last night, it's the that comes with the main game, not the smuggling one. It's the one that 4 counters on the shuttle.

It's not really complicated

Nexu/Vader may only use one offensive or Attack'y action. So using Vader: if he does a normal Attack he may not use Brutality afterwards. He may use Firce Choke since that is not an attack. Likewise he may start with Brutaliy (if he has 2 eligible targets) but hen he may not do a normal Attack. He may use Force Choke (as the other. Example)

Same goes for Nexu

E-Webs text overrule the normal limit. Which is fair since it may not atta k if it voluntarily has moved

And the tokens in that mission is face (colored) side down to begin with so their value is 2 until flipped

Firstly the Skirmish rules say that you only get one attack. If that is the case, why do some character cards give models to attack twice? I did wonder if it due to those cards also being used in the Campaign, but given that there are smaller card versions for the main characters I couldn't see that as being correct, am I missing something?

From the Skirmish guide:

Attacking: Figures can only use one of their actions to attack per activation. This includes using special actions that involve performing one or more attacks (such as the Nexu's 'Pounce' or Darth Vader's 'Brutality').

In the mission with the 4 counters on the shuttle (sorry don't have the details to hand) if refers to flipping them, but gives no more information. Are they supposed to start face down (greyside up)? Do they all have to be the same colour? It's a bit vague (unless I'm missing something here)

For the attacks question, see the above responses, they covered it. You can only perform 1 action that creates an attack/attacks per activation. So when you Brutality with Vader, you get to make two attacks (using conditions from the card) but afterwards you cannot take any action which would cause another attack.

Note: if you are given attacks outside of the figure's activation, they do not count against the limit. So you can, say, Brutality with Vader during his activation, and then later in the round use the Elite Imperial Officer to grant him an out of activation attack.

Also, it is worth noting that a golden rule of gaming is that "Cards trump rules". Meaning if the rules say one thing and a specific card tells you to do the opposite, the card wins. Basically the rules are "general" and the cards are "specific". Specific > general. Some examples would be the E-Web Engineer or Fenn Signis. They both have the ability Assault, which allows them to attack more than once per activation. Cards trump rules, so both can do so, despite what the rules say.

For the second question, the tokens start colored side down and can be flipped up. The color doesn't matter, just that you can tell whether it is face up or down. I personally like using the Red/Blue tokens since they are bright enough to be very obvious to both players.

As far as attacking twice, There is a Golden Rule (In the first few pages of one of the books...not sure which one) that says Cards will occasionally overrule the actual rules.

For example the E-Web says it may perform multiple attacks on its turn, which overrules the actual rules.