CR and level are not the same.
The stat blocks in the Monster Codex use the rules from the Bestiary for Advancing Monsters by adding class levels.
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Ah, the Bestiary has two different sections about adding class levels to monsters. I believe you're looking at the information on pages 313–314, which refer to playing a monster as a PC (a player resource, so to speak). I instead encourage you to look at the Adding Class Levels section on pages 296–297, which is directed toward the GM. In particular, look at Step 3, which details how one calculated the challenge rating of a monster with class levels added. It's important to take into consideration the monster's key role (combat, spell, skill, or special in Table 2–4) and the type of class added.
For example, the Frost Giant Hunter on page 71 of the Monster Codex is a 2nd-level ranger. Looking at table 2–4, ranger is a combat role, and frost giants are combat creatures. That means every level adds 1 to the CR (9+2=11). Now turn the page to the Frost Giant Ice Mage. Since sorcerer is not a combat role, a certain number of the sorcerer levels (in this case all of them) only add 1/2 each to the CR (9+[6/2]=12).
CR and level are not the same.
The stat blocks in the Monster Codex use the rules from the Bestiary for Advancing Monsters by adding class levels.
That was what I got told as well when I noticed this. The best way they could have clarified it would have been by writing down the creatures' roles, like telling us which one in Combat, Skill, Spell and Special.
That way, it would have given a faster reference on why this creature has more class levels but a lower CR.
From the looks of it, all 20 creature groups fill the Combat role... except maybe vampires, since it's a template, not an actual creature.
You are correct, they are different things.
But they SHOULD in my opinion relate. CR is supposed give an estimate of a challenge for characters of a certain level. The different rules for calculating CR and Level annoy me :)
Example: Lets say a party of 4 people all made Serpentman Wizards.
10th level wizard + serpentman is level 12.
They gang up on a single 10 level wizard serpentman CR 14.
CR 2 levels above the party level should be a challenge, it obviously would not be. I would thus prefer a unified way of adding to the CR and to the player.
If you want a challenging fight then don't use one monster. A CR X fight using one monster, is easier than one with the same CR made up of multiple monsters.
Also the the creature roles are in the bestiaries, along with the rules for how they work. There is no need to explain it again in another book since they don't explain it in other published products.