I got wise to this fare class thing many years ago when helping Mum understand crediting MH flights to Enrich.
In those days, and still now, the type of fare class you purchase affected the number of miles you obtained (and also status, since status on MH is measured in mileage). Some fares in those days didn't earn any miles at all (a la SQ until of late, and of course MH now offers Enrich miles on all fares, albeit a pittance on some).
My Mum found out the hard way and until I did some scouting it took me a while to realise what was going on. After that, we always made sure to check the fare class (though for Mum, fare class or not, the lowest price is the lowest price...)