@ASalas Also adding to pasfans01 answer 2., keep in mind that if you want to use NDVI for data assimilation puproses (e.g. compute vegetation biophysical parameters etc.) you will need the Surface Reflectance (Level 2A) data to produce the NDVI map, since 2A are more close to the true radiance values. For more information, you could read the sentinel 2 users guide that ESA offers. If you use the 2A data, in your case it would be of great help to first check the quality assesment data in order to see and assess the impact of cloud coverage in you scene.
Regards
