It is shown that the singular set for the Yang-Mills flow on unstable holomorphic vector bundles over compact Kaehler manifolds is completely determined by the Harder-Narasimhan-Seshadri filtration of the initial holomorphic bundle. We assign a multiplicity to irreducible top dimensional components of the singular set of a holomorphic bundle with a filtration by saturated subsheaves. We derive a singular Bott-Chern formula relating the second Chern form of a smooth metric on the bundle to the Chern current of an admissible metric on the associated graded sheaf. This is used to show that the multiplicities of the top dimensional bubbling locus defined via the Yang-Mills density agree with the corresponding multiplicities for the Harder-Narasimhan-Seshadri filtration. The set theoretic equality of singular sets is a consequence.