First note that, rules guru or no, the official rules of D&D 3.5e do not ascribe any rules authority to the Rules of the Game articles. In the case of a contradiction between them and the official published books, the books officially win. And this makes sense, because the official books would have seen much more editorial love than the Rules of the Game articles. In this way, the Rules of the Game articles are in a similar boat to the FAQ.
On the other hand, yes, the Rules of the Game enjoyed a far higher accuracy rate than the FAQ did, at least in my experience, though I cannot claim to have gone through both and carefully tallied how many mistakes are in each. It’s just my impression that I’m fairly often saying “the FAQ is wrong” while I’m also often saying “the Rules of the Game aren’t official rules sources, but in this case it’s accurately describing what the official rules say.”
But it’s definitely not 100% accurate, which to me means there’s not much point in referencing it: since you need to double-check against the rules anyway, why bother with the Rules of the Game articles? Anyway, since there was a request for times when the Rules of the Game articles were wrong, here are some:
Rules of the Game and Two-Weapon Fighting
In this answer, I go through the Rules of the Game articles about two-weapon fighting: a complicated part of the rules, often confused, and well worth discussing and clarifying. Skip gets most of it right, but there are at least a couple of errors, one rather egregious:
Using separate weapons for separate attacks when not using the two-weapon fighting combat option (admittedly might just be an artifact of sticking to the simplest base case of someone at 1st-level with no extra attacks).
You do not have to choose between the attack and full attack actions until after you have made your first attack on your turn (see page 143 in the Player's Handbook). However, if you intend to attack with two weapons during your action, you must take the correct penalty for each attack or give up your opportunity to use your second weapon (because the rules require you to take a penalty on attacks you make with both your primary and off hands).
(emphasis mine, though the italicized Player's Handbook is present in the original)
[...] Skip here implies that the torch is unavailable even if you have attacks for other reasons (high BAB, haste spell, etc), but if that implication is intentional (rather than just an artifact of assuming level 1 without special features as a base case), then he is wrong.
No TWF feats on non-thrown ranged weapons: simply and objectively wrong, the official rules say nothing of the sort and it would make absolutely no sense with, e.g., hand crossbows.
Ranged weapons you don't throw use most of the rules for two-weapon fighting; however, the Two-Weapon Fighting feat and related feats don't apply to ranged weapons that aren't thrown.
Just another example of Skip being wrong. This rule is not present anywhere in the actual published rules, it's literally something he appears to be making up for the purposes of this article. Under the official rules, this should be ignored as an error.
Double weapon inconsistency—in this case, this was almost-certainly a mistake in the rules as written that was missed in editing, and then missed again when Skip wrote this article. But the official rules as written specify that double weapons act like a one-handed and light weapon pair for attack penalties only—which means for other purposes (like damage bonuses) they still count as two-handed weapons. Considering the existence of a prestige class that offers exactly that as its capstone benefit, it seems very much that Wizards’ impression of the rules matches Skip’s, so it’s hard to blame him. Still, it would have been nice for Skip to have noticed and pointed out the inconsistency (and even nicer for it to have seen errata).
Mentioned only for completeness, this article does not discuss off-handedness in any meaningful way that wasn't already covered in previous articles.
Just as another example of Skip being wrong, though this one is much more dubious:
*The damage bonus for the double weapon's primary end is +3 Strength, +2 enhancement, +2 weapon specialization. The damage bonus for the double weapon's off-hand end is +1 Strength (1/2 of +3) and +2 weapon specialization.
The rules do not actually state at any point that double weapons are treated as a one-handed weapon and a light weapon for the purposes of damage. They state they behave like a one-handed weapon and a light weapon for the purposes of attack rolls but say nothing about damage rolls. By a strict reading of the rules, you actually get 1½ Strength to both ends. This is likely an oversight, however, so this particular “mistake” may be more with the PHB's editors than with Skip. Still, if the goal was to clarify the rules as written in the PHB (which is nominally the purpose of the articles, and certainly the only valid thing for them to do under the errata rules), then this is another error.
Finally, note Wyrmwood’s comment on that answer:
Heh, I thought to myself "this doesn't make sense, he's reading a different article". Well, he is :) Evidently, the Rules of the Game articles on this topic were updated (and the first mention of changing handedness clearly can't work with any notion of 'weaker handedness'). Oddly the old articles can still be downloaded from the same page as a pdf. The HTML is the updated version that forgoes any mention of the penalty during an attack of opportunity (where TWF penalties do not occur). – Wyrmwood Oct 28 '13 at 1:51
Simply running across out-of-date and inaccurate versions of the Rules of the Game articles and the confusion that results from that is, itself, a pretty good reason for them to have a poor reputation.