What complications are associated with a chondral transplant from my knee to my toe?

Lots. You could have a number of complications in your knee such as infection, swelling, pain, arthritis, etc. You could also have the same complications in the toe in addition to the toe not improving. Talk to your surgeon for more information.
Several are possible. Chondral transplants from the knee to other joints are relatively rare procedures. Complications include surgical site infection, donor site (knee) pain, failure of graft incorporation, continued foot symptoms, and knee joint degeneration, among others. Due to the rare nature of that procedure there is not a lot of literature on the success rates or complication rates.