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I've had this problem for awhile now. When deconstructing monsters from the various Monster Manuals (to modify or add templates etc) their skill ranks do not add up properly.

Am I missing something, doing something wrong or is this simply an example where the Primary Source rule is changing the monsters without stating it's doing so?

As an example, let's take the loyal dog Monster Manual pg 271.

His stat block shows:

Abilities:

Str 13, Dex 17, Con 15, Int 2, Wis 12, Cha 6

Skills:

Jump +7, Listen +5, Spot +5, Survival +1*

Dogs Have +4 Racial Bonus to Jump

* Dogs have +4 Racial Bonus to Survival when tracking by scent.

It's easier to word this question by building the skill stats from the ground up rather than deconstructing so I'll do that here just to make it read easier:

Spot: +1 Wis, +2 Alertness =+3 (before spending ranks)

Listen: +1 Wis, +2 Alertness =+3 (before spending ranks)

Survival: +1 Wis=+1 (before spending ranks)

Jump: +1Str, +4 Racial Bonus AND +4 speed (untyped) bonus since he has a 40' movement. (See link for explanation if your unfamiliar)=+9 (before spending ranks)

The only other explanation I can see is that they ignored the speed bonus to jump while giving him an extra 3 skill points to spend.

So, back to my question:

Am I missing something, doing something wrong or is this simply an example where the Primary Source rule is changing the monsters without stating it's doing so?

You are correct that a great many creatures' skill points are inaccurately spent (cf. this question). Other errors, too, exist in creatures' stat blocks (cf. this question). Errors like these can remain uncorrected even by errata and reprints like the premium edition Monster Manual (2012)) that include stealth errata: its dog entry has the dog's Jump skill bonus also as +7.

If you tinker long enough, you'll likely find some error or important omission in—at a guess—about every third monster. (That's what it feels like to me, anyway, and I tinker with a lot of monsters.) And, of course, the more complex the monster, the more likely it is that there's an error somewhere. You've to adjust things and move on. Then, if you're feeling generous, share the error with your players and have a laugh. You may even get lucky and the topic will arise naturally in another venue—like on a Q & A site, for instance—allowing you to share your findings more widely

If this minutiae really interests you, Cooper's Compendium of Corrected Creatures (with which I am not affiliated but which I endorse) goes through the entire SRD and attempts to fix many of the more egregious errors therein, and Corrected Creatures does, indeed, change the dog's Jump skill bonus to +9.

Creature statblocks had errors (or, if being generous, unmentioned specific-trumps-general exceptions) all the time in 3.5e. They are not generally worth trying to back-calculate.

I cannot see anything wrong, at a glance, with your reasoning. It certainly seems like the dog’s Jump check is off.