Both NDVI products use the same algorithms, i.e., BRDF modelling and CV-MVC compositing. The only difference is the data input. Terra circles a morning orbit and Aqua an afternoon orbit, which causes differences in solar zenith angle (also sensor view angle and azimuth angles) for daily MODIS images.
According to my experience, both products perform very similarly for vegetation change detection. In an early version (C005), the Terra MODIS suffers from calibration issues, and the NDVI product is less accurate. But in current C006 version, the products are more comparable.
The subtle differences can be caused by any factor that affects image acquisition, e.g., cloud coverage, solar angle and observational geometry...
Also, if you search on Google Scholar, you'd find that there are a number of publications that tested both products in terms of comparison of derived indices.
Both NDVI products use the same algorithms, i.e., BRDF modelling and CV-MVC compositing. The only difference is the data input. Terra circles a morning orbit and Aqua an afternoon orbit, which causes differences in solar zenith angle (also sensor view angle and azimuth angles) for daily MODIS images.
According to my experience, both products perform very similarly for vegetation change detection. In an early version (C005), the Terra MODIS suffers from calibration issues, and the NDVI product is less accurate. But in current C006 version, the products are more comparable.
The subtle differences can be caused by any factor that affects image acquisition, e.g., cloud coverage, solar angle and observational geometry...