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We overview the methodological challenges in developing coupling schemes of coupled Computational Fluid Dynamics (CFD) and Discrete Element Method (DEM) to tackle of a class of engineering problems involving complex multi-phase, multiway interactions among granular particles, single or multiphase fluids, and possible structures. Taking four different engineering problems as examples, we discuss the applicability of either unresolved or fully resolved coupling scheme of CFD-DEM for practical use and the advantages of a hybrid scheme of them. The examples include (1) debris flow impacting on a rigid or flexible resisting barrier; (2) coastal wave/tsunami sloshing with breakwater and coastal levee structures; (3) laser powder bed fusion in addtive manufacting; and (4) granule tablet melting. We showcase situations where accurate modeling of particle shapes or consideration of multiphysics processes such as phase transformations become important and how the related computational challenges are tackled in CFD-DEM simulations.