FFT Multiple Response for time T
You typically do a spectral analysis on a time series that has a single value per time instance. For example: what's the distance a car has driven after 1 hour. The answer can be 10 km or 50 km but it can't be both at the same time. 

We first we need to understand WHY is there more then one value at the same time

Sometimes data can have multiple dimensions. In our example above you can express the position of the car in x, y, &amp; z co-ordinate in which cases you have 3 values at the same time. In this case you would can analyze each dimension individually or you can derive a single quantity that you are actually interested in (like the total distance).  

It could also be statistic, you have multiple estimates for the same data point. You could reduce this by taking the mean or doing a Monte-Carlo type of analysis. 

Can you elaborate on the type of data and the reason for the multiplicity?