We examine scatter and bias in weak lensing selected clusters, employing both an analytic model of dark matter haloes and numerical mock data of weak lensing cluster surveys. We pay special attention to effects of the diversity of dark matter distributions within clusters. We find that peak heights of the lensing convergence map correlate rather poorly with the virial mass of haloes. The correlation is tighter for the spherical overdensity mass with a higher mean interior density (e.g. M1000). We examine the dependence of the halo shape on the peak heights, and find that the root mean square scatter caused by the halo diversity scales linearly with the peak heights with the proportionality factor of 0.1–0.2. The noise originated from the halo shape is found to be comparable to the source galaxy shape noise and the cosmic shear noise. We find the significant halo orientation bias, i.e. weak lensing selected clusters on average have their major axes aligned with the line-of-sight direction, and that the orientation bias is stronger for higher signal-to-noise ratio (S/N) peaks. We compute the orientation bias using an analytic triaxial halo model and obtain results quite consistent with the ray-tracing results. We develop a prescription to analytically compute the number count of weak lensing peaks taking into account all the main sources of scatters in the peak heights. We find that the improved analytic predictions agree well with the simulation results for high-S/N peaks of . We also compare the expected number count with our weak lensing analysis results for 4 deg2 of Subaru/Suprime-Cam observations and find a good agreement.