So torch is たいまつ, and is written in kanji as 松明. Matsu, however, means pine, which is the first kanji, not the second. Are there many words like this in Japanese that seem "out of order"? Is there a reason or way to predict this phenomenon?
I have long enjoyed Shogakukan's Kokugo Dai Jiten (KDJ) for its etymologies -- it's one of the few monolingual Japanese dictionaries to include etymologies for its terms.
This post relies on their entry for 松明, available here at Kotobank.
Derivation of the term たいまつ
The たいまつ reading is first cited to the 宇津保【うつぼ】物語【ものがたり】, dated to around 999. Unfortunately, I cannot confirm the first date of this reading applied to the 松明 spelling.
This たいまつ term was apparently a shift from older たきまつ, where まつ was the regular noun 松【まつ】 ("pine"), and たき was the 連用形【れんようけい】 (continuative or stem form) of the verb 焚【た】く ("to burn something"): 焚【た】き松【まつ】, literally "burning pine, pine for burning".
So far as I've been able to find so far, dictionaries don't have any entry for 焚【た】き松【まつ】, but I think it's safe to guess that that form of the word is even older.
Odd kanji spellings: jukujikun
As you noticed, this spelling seems backwards compared to the reading -- the 松 character comes first, but the まつ reading comes second. This is due to a practice known as 熟字訓【じゅくじくん】, which basically involves spelling word A with the kanji for word B. Both words A and B are usually at least in the same ballpark, meaning-wise.
More at Wikipedia, in the "Special readings" section of the "Kanji" article.
Derivation of the spelling 松明
This is clearly 松 ("pine") + 明 ("bright; light"). Read with the 音【おん】読【よ】み, this word is しょうめい. This spelling with the しょうめい reading (actually, the earlier せうめい reading) is first attested in 1305.
I suspect this was used as a pun with the word 照明【しょうめい】 ("illumination, lighting", also earlier read as せうめい), which itself is first attested in around 1060 (per the KDJ entry here).
So we have a word 照明【しょうめい】 ("lighting") (1060), and pine torches used as lighting and spelled 松明 and read as しょうめい (1305). This spelling was then used for the "pine torch" term たいまつ, while keeping the たいまつ reading as a kind of jukujikun (??? -- first date for this is uncertain, as noted above).