Control point generators are not very good at distinguishing between static objects, such as buildings, and objects that change quickly such as waves, foliage, clouds and people. This causes alignment problems, especially with clouds that can easily move several pixels between shots.
Celeste is a new tool in hugin that has been trained using w:Support vector machine techniques to identify clouds in photos and remove control points from these areas. This functionality is available in the Hugin Images tab and described in the Using Celeste with hugin tutorial.
celeste_standalone is a command-line tool with all the same functionality as Celeste in hugin. It has many options, but at its simplest can be used to just 'clean' an existing project file:
celeste_standalone -i project.pto -o project.pto