Images that capture only water cannot be calibrated (optimize internal and external orientation of the camera). The reason is that it is very hard to find keypoints on water surfaces (water is very uniform). Even if keypoints are found, it is very hard to match them between images, as these points are not static (water moves).
Since the images that contain only water do not get calibrated, they do not contribute at all to the processing and can not be used to give color to the orthomosaic. Therefore, there might be holes (lack of information) in the orthomosaic on water surface areas.
It is suggested to take images that contain water with some land (30% of land minimum). In this case, the images could get calibrated and contribute to the orthomosaic generation. For more information about how to map water surfaces: Step 1. Before Starting a Project > 1. Designing the Image Acquisition Plan > a. Selecting the Image Acquisition Plan Type.