I think the batch image gen has an issue when the workflow generates more than one image per execution. Specifically the line
File.WriteAllBytes($"{output_folder}/{preExt}.{ext}", image.Img.ImageData);
at line 199 ImageBatchToolExtension.cs
I think can get called multiple times during a single gen (such as when extracting faces) and the generated images just overwrite each other. I think the metadata has a unique index count in it that could be appended maybe? The multiple images show up in the UI as unique, it is just the writing to the output directory that is an issue.