I came across few papers that implanted both on the medial and lateral condyle and comparing the regenerative property of certain scaffolds/constructs. But wont it affect the result since these two locations have different load bearing?
it will certainly affect. Every region is not load equally load bearing region. Many people tests their material on defects made non-load-bearing in the beginning at least.
It is very well possible that cartilage "repair" (more accurate is fibrous like cartilage formation) is easier in non load bearing regions of the joint. It is generally easier for the construct to stay on place and the dynamic mechanical stimulation is not affecting the constructs (most of the time they have very limited mechanical properties).
However, what is the relevance of these test? If you consider that cartilage is highly demanding on mechanical forces for its maintenance, these testes on non-load bearing regions show low physiological relevance in my opinion.