Only people on visas valid for MORE than 6 months have to pay the IHS surcharge. The fiance visa is only valid for 6 months, so there was no surcharge to pay when you applied.
However this does mean that she is not currently covered for any 'free' NHS care and will have to pay the full cost for any non-emergency treatment she receives. If she has health insurance, she will pay 100% of the cost. If she does not have health insurance, she will be charged 150% of the cost.
It's her responsibility to make sure she is charged for treatment (as the NHS is not used to charging people and often will tell someone they don't need to pay when actually they do). She must also make sure she pays any outstanding NHS bills before she applies for FLR(M), as an unpaid NHS bill of £500 or more is an automatic visa refusal.
When you apply for FLR(M), you will pay the IHS surcharge for the full length of the visa (2.5 years), which is currently £1,000 (2.5 years x £400/year).. though this is supposed to increase to around £600/year around October. The visa cannot be granted unless the full IHS surcharge has been paid, which is done as part of the online application.