I've worked with image processing for a good period of time (plant related researches)
maybe the most challenging thing is (in my opinion) the consistency and stability of light source during each photo section and throughout the project.
especially when using this technique to process color related traits
During image processing, major challenges can come across during various stages which can be categorized by factors affecting image acquisition, processing and analysis; image pre-processing; and image segmentation.
These challenges can be rectified with proper assessment methodologies.
Since Image Processing is a big domain, challenges associated with it cannot be summarized in one answer, but I have one short paper focused only on challenges of Image-based systems in event processing domain: https://dl.acm.org/citation.cfm?id=3095095
We may consider the challenges from different viewpoints connected to the application domains. Medical image processing domain has its own hot topics with respect to segmentation and classification, while image processing with an emphasized focus on Biometrics imposes different challenges in feature extraction, features matching, and features storage and retrieval. In computer vision, object detection and segmentation in a crowded environment is still a hot topic. Secure image processing and secure transmission is another domain that holds its own challenges as well.