1) Overvaluation. Overly optimistic assumptions used in the valuation process. Either in the form of overly optimistic cash flows or a willingness to pay to high a multiple for perceived synergies that never materialize.
2) Cultural / Operational differences that were not adequately researched/identified in the due diligence process. Moral is easily eroded in the acquired company if management does not get on board early to communicate with managers of the acquired company.
3) Lack of planning and strategy for the after closing operations of the combined entities. To much focus is put on getting the deal done with not enough emphasis on how things are going to play out after the close date.