Q: What is the difference between research implication and recommendation?

You cannot really be sure that your paper was rejected because you disagreed with just one statement of the reviewer. The reviewer just provides his/her comments on your paper; it is ultimately the editor who decides whether to accept or reject a paper. 

Possibly, the reviewer felt that it would be more appropriate to include research implications rather than recommendations in your paper. Research implications suggest how the findings may be important for policy, practice, theory, and subsequent research. Recommendations, on the other hand, urge specific actions to be taken with regard to policy, practice, theory, or subsequent research. It is possible that your research did not have strong enough evidence to support the specific recommendations that you made. Instead, a more generic approach, explaining how your research results could be important for policy, practice or theory would probably be a more suitable approach.

Recommended reading:

• In a manuscript, are the Discussion and Conclusion sections the same?
• Tips for writing the perfect IMRAD manuscript
• The secret to writing the results and discussion section of a manuscript