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Machine learning (ML) has become a popular technique for various automation tasks in the era of Industry 4.0, such as the analysis and synthesis of visual data such as images and videos, natural language and speech, financial data, and biomedical applications. However, ML-based automation techniques are facing difficulties like decision-making, thus incorporating user expertise into the system might be advantageous. The goal of adding human domain expertise with ML-based automation is to provide more accurate prediction models. Human-in-the-loop (HITL) systems that integrate human expertise with ML algorithms are becoming more and more common in various industries. However, there are a number of methodological, technical, and ethical difficulties with the development and application of HITL systems. This paper aims to explore the methodologies, challenges, and opportunities associated with HITL systems implementations.We also discuss a number of issues that must be resolved for HITL systems to be effective, including data quality, bias, and user engagement. Besides, we also explored several approaches that can be utilized to enhance the performance of HITL systems, such as active learning (AL), iterative ML, and reinforcement learning, as well as the current state of the art in HITL systems.We also selectively highlighted the advantages of HITL systems, such as their potential to increase decision-making process accountability and transparency by utilizing human experience to improve ML decision-making capability. The paper will be very useful for researchers, practitioners, and policymakers.