You can add comments directly in the Rejection section that appears when you choose the Reject action on the recommendation.

This comment box is displayed as a mandatory or optional field (based on configuration) to ensure a clear guidance before sending back the recommendation.

During rejection, rejection comments can be entered in the Confidential Notes, and the same is visible for the manager in the system.

PS: Synergita implementation for your Organization may vary from how the features are described here. The screen shots given here may also be different from what you see in your system. Please talk to the concerned person in the Organization for any specific queries.