This is a really difficult question because the answer will depend on the individual and specific imbalances/compensations. Some global issues that can be caused by cycling are quad dominance and tight hip flexors which could lead to some low back issues. Foam rolling and stretch quads and hip flexors and strengthening glutes and hamstrings can counter a lot of those issues.
The knee is basically a hinge and it gets told where to go by the ankle or hip so individual issues with knee tracking could come from limitations in ankle or hip mobility which are better addressed by a trained professional in person.