About morphology: 列車 is a compound noun made up of two morphemes, with the head being 車. According to Chaofen Sun’s ‘Chinese: A Linguistic Introduction’ (p. 50), about 90% of compound nouns in Chinese have the head (nominal formant) on the right. Thus the structure of 列車 is not unusual at all. The morpheme on the left tells us what kind of car it is, as in similar compounds like 汽車, 公車, 三輪車 etc. It’s just a coincidence that 列 also happens to be used as a classifier. (So @Rephinx is correct.)
About etymology: steam engine trains were only invented in the 19th century, so this word won’t be very old. It’s instructive here to look at the origins of the English word ‘train’. (See link here: http://www.etymonline.com/index.php?term=train)
‘Train’ comes from a Latin root meaning ‘pull, draw’, which is quite similar to the meaning of 列. It seems that 列車 is a kind of calque on the English word.
Generally Chinese word formation is an interesting topic. Besides Sun, I would recommend Jerome Packard’s ‘The morphology of Chinese: a linguistic and cognitive approach’ (Cambridge UP 2000), although parts of it make use of X-bar theory and thus might be difficult to follow if you don’t have a background in linguistics.