You have a few misunderstandings, which explains the discrepancies that you see.
To begin, Seoni does not have the ranks you think she has. The bonuses listed for her account for all bonuses to those skills, not just ranks. Namely, her lizard familiar gives +3 to Climb, which accounts for the entirety of the +3 bonus listed for her, so she has zero ranks in that.
In addition, Alertness adds +2 to Perception and Sense Motive, and World Traveler adds +1 to Diplomacy, Knowledge (local), or Sense Motive and makes the chosen skill a class skill. These are both Wisdom skills, so +1 for 13 in that, for +3 Perception and +4 Sense Motive. So zero ranks in these skills, too. Note that Sense Motive is a class skill for her, thanks to World Traveler, but she doesn’t get the +3 because she doesn’t have the 1 rank.
Furthermore, human racial traits include an extra 1 skill point per level, so that brings Seoni to 3. And anyone may choose to get +1 skill point per level when taking a level in their favored class,1 which would bring her to 4, but Seoni has instead elected to take the +1 HP (hence her 1d6+2 with only Con 12).2
Finally, Seoni’s arcane bloodline adds any one Knowledge skill as a class skill. In this case, Seoni’s choice was Knowledge (planes), and that explains the +4 bonus.
Thus, Seoni has 3 skill points (two from sorcerer, one from human), in Bluff, Knowledge (planes), and Spellcraft.
Humans may have any one class as their favored class; for Seoni, that’s clearly sorcerer.
Other options are defined for a particular race/class combination, such as the “Add one spell known from the sorcerer spell list. This spell must be at least one level below the highest spell level the sorcerer can cast” option added by Advanced Player’s Guide for human sorcerers. But the 1 HP or the 1 skill point are always options.
As a complete aside, everything figuring all of that stuff above was hard—I originally couldn’t account for the Perception and Sense Motive bonuses because I forgot Seoni had Wisdom 13 (thanks to @user28605’s answer for pointing it out). And I have an awful lot of familiarity with these rules.
Ultimately, the iconic characters are meant to just be played, as is, often by the GM as an NPC. They aren’t really useful for trying to understand the game, because they don’t break down which bonuses come from where. Even playing as Seoni would get quite difficult the moment she levels up, since then you would need to know about her skill ranks.
So I would suggest that trying to understand a completed character’s final stats and reverse-engineer where all of the bonuses came from is a very difficult, time-intensive process. If you are new to the game, it probably isn’t worth trying to do it.