Typically this is because it is relatively easy to assign time allowances to all the activities that have been thought of, but it is the ones that have not been thought of that take the extra time. However, there is also a tendency to be optimistic otherwise the project might not get approved, or "tight schedules" are a means to keep the pressure on the project team.
Many delays arise from things that are necessary but were overlooked in preparing the plan. Even more delays are due to risks that were either not fully appreciated or disregarded during planning. The biggest and most damaging delay invariably stems from failing to start promptly the whole project or one or more of its major activities.