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A major obstacle to the application of the standard Radial Basis Function-generated Finite Difference (RBF-FD) meshless method is constituted by its inability to accurately and consistently solve boundary value problems involving Neumann boundary conditions (BCs). This is also due to ill-conditioning issues affecting the interpolation matrix when boundary derivatives are imposed in strong form. In this paper these ill-conditioning issues and subsequent instabilities affecting the application of the RBF-FD method in presence of Neumann BCs are analyzed both theoretically and numerically. The theoretical motivations for the onset of such issues are derived by highlighting the dependence of the determinant of the local interpolation matrix upon the boundary normals. Qualitative investigations are also carried out numerically by studying a reference stencil and looking for correlations between its geometry and the properties of the associated interpolation matrix. Based on the previous analyses, two approaches are derived to overcome the initial problem. The corresponding stabilization properties are finally assessed by succesfully applying such approaches to the stabilization of the Helmholtz-Hodge decomposition.