Michael,
instead of using an upwinding scheme, you can also enlarge your dispersion. This should also work and maybe you have more controll over your computation.
The theory of numerical computations would tell you that your simulation should be stable if you use mesh Peclet numbers smaller or equal to 1. (The mesh Peclet number is defined: Pe = ds / alpha, where ds is the length of your element edges and alpha your logitudinal dispersivity).
To my experience you can accept Peclet numbers up to 2, but beyond that numerical problems may begin.
So there are 2 things you can do: assume a higher longitudinal dispersivity (if you do this, you should also enlarge the transversal dispersivity; ratios od longitudinal/tranversal 5:1 - 10:1 should be ok) or refine the mesh.
Nomally the most critical parts of the simulation are arround your transport boundaries where you start the simulation with high concentration gradients. So maybe a mesh refinement arround your wells could help.
Zebra