Ok so there's a difference between class levels and character level. Class levels is how many levels in a class you took. Character level is the combination of all the levels you took in a class. For me, who took 3 levels in Soldier, they are the same number. For people who are multiclassing, like you, they are different. Your character level is 3, but your class levels is 2 for Scout, and 1 for Scoundrel. When you gain class levels, you get things from that class (talents and bonus feats.) When you gain character levels, you get things based on your total character level (feats every 3 levels, ability score increases every 4 levels.)
So here's the breakdown, at level 1 you took Scout and got the defense bonus, starting feats, and the talent from your class. For having a character level of 1 you get a feat. At character level 2, you took 1 class level in Scoundrel. This means you now have class level 1 in Scout and 1 in Scoundrel, but your character level is 2. Character level 2 doesn't give you anything but class level 1 in Scoundrel gives you the starting feats, defenses and talent from Scoundrel.
Now you go to your 3rd character level. You took a 2nd class level in Scout, which if you look at the Scout class, means you get a bonus feat. This is for your 2nd class level in Scout. That's all you get from that. However, you are character level 3 now, which means you get a feat.
1: Racial bonuses/1st level feat
3: Feat (any)
Scout 1: Defenses/Scout Talent 1 (From Scout Talent Trees)/Class Feats
Scoundrel 1: Defenses/Scoundrel Talent 1 (From Scoundrel Talent Trees)/Class Feats
Scout 2: Bonus Feat (Scout List)
So you get Shake it Off/ Your Weapon Proficiency Feats/Point Blank Shot for free from Classes. And a feat from first character level of your choice. And then at 3rd character level you get two feats, one from character level 3 and one bonus feat from Scout level 2 (from the Scout bonus feat list.) That's your feats.
You get one Scout talent and one Scoundrel talent. They have to be from the respective talent trees of each class. So you'll have to drop one of your Scout talents and pick a Scoundrel talent in it's place.