We are sorry to hear you are not happy with your results. Water will cause huge problems in the rendering as noted as item number 1 in our Data Collection guidelines:
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Minimize the Inclusion of Water
Always in motion, highly reflective, and transparent, water has a lot of properties that make it hard to render well.
Large areas of open water will not likely process well in any photogrammetric application. While it may turn out well enough in a 2D ortho map, water rarely renders well in the 3D outputs and can add unsavory motion related artifacts. If you must include water in a survey area, try to keep some shore structure in place to give our processing something to hold on to.
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If it worked previously you should count yourself as being lucky. It could have been that the time of day provided less sky/sun reflections or the surface conditions may have been different. For relatively small bodies of water like that it can help to fly a bit higher such that all of the images will have at least half of the image with land that has fixed features to match with. That isn't always helpful though. You could try running it as a Flat Map since that doesn't rely on feature matching to make the map.
