Hunt for predatory journals is based on binary division of the publishing world to legitime and predatory journals. This leads to difficulties in labeling publishers like MDPI with questionable practices. However, the root cause is not the publisher itself but the problems in the peer review system. These problems have created markets for the for-profit publishers shaking the understanding of conservative researchers and their belief about what is good science. In this paper, we analyze the problems via examples based on our own experience as author, reviewer, guest editor, associate editor, and editor-in-chief. We discuss how MDPI has addressed these problems.