Eggs were set upright, with small end up. Eggs placed upright in the incubator should always be set with the large (air cell) end up.
Advancing breeder hen age and shell quality problems.
Egg turning frequency and angle were not adequate. Regular turning of the egg through a minimum 45 degree angle assists the embryo to position for hatch. Eggs should be turned at least 3 times daily, though more is better.
Inadequate percent humidity loss of eggs in the setter. Acceptable weight loss of eggs during incubation is 11-14%.
Inadequate air cell development, incorrect temperature and humidity regulation and insufficient ventilation in the incubator.
Imbalanced feeds, elevated levels of mycotoxins, and vitamin and mineral deficiencies.
Exposure to lower than recommended temperatures in the last stage of incubation.
Round shaped, or overly large eggs.
Eggs handled, or stored improperly.
These are the most common reasons for malpositioned chicks I've just copied it from the learning centre. I've always believed the most common reason is eggs set in the bator with the pointy end up when they should be fat end up. But as you can see from the list it can be many factors that cause malpositioned chicks.