Can you develop cognitive problems from being on cell cept for too long?

Uncertain. Some transplant recipients report loss of certain abilities such as fast counting, reading, diminished sensations or perceptions. Whether this is due to their actual cause of organ failure, other co-morbidities, or the drugs they are given to suppress rejection (such as mycophenolate mofetil) or treat other problems, is very hard to pin point clearly.
Maybe. Cellcept (mycophenolate mofetil) is not known to cause cognitive defects but no one can guarantee that it doesn't. Cognitive problems are more likely due to a separate process or side effects from other medications which you may be taking. The best course would be to return to your transplant center and discuss your issues with a transplant physician familiar with the drugs you are on.