Yes, and in distance based mileage earning, you will earn less miles because they will credit you the "direct' mileage. Insult t injury if you thought it was non-stop. I.e. if you flew a direct flight JFK-LAX with a stop in MIA, it would earn the direct mileage of 2475 rather than 3432 actual flight miles.
And though FTers generally know this distinction, I 100% agree it is confusing to most people.