OP, it seems like you are not SPG Plat or Gold and what you ended up was a suite, is this correct (did it have a round bed)?

SPG 50 reservations are same as best flexible rate but cannot be booked online - you must call (so there is nothing wrong with the website).

It a bit odd that you did not check the room rate at the time of the check-in. I am a frequent guest at the W Seoul and every single time I stay there the check-in agent reverifies the stay rate for me (and I've also used SPG50 rate many times here and had no problem).

Studio suite goes for around 800K Won at a rack rate. So, it does seem like the SPG agent booked you a suite (by accident or that may be the only SPG50 rate available and the agent mistakenly told you that lower rate was available). Regardless of being charged at the time of reservation, you should have re-verified your rate at the check-in.