During a cow's eye dissection, the lens of our eye was brown instead of clear, why might that be?

It's probably because of the preservative used for the eye. Preservatives like formaldehyde work by cross-linking proteins - basically by altering their structure and fixing those proteins in place. The lens of the eye is full of a protein called crystallin. It's clarity and optical properties are the result of the structure of that protein. When the formaldehyde (or other preservative) altered that protein, it also altered its optical properties.