Injury during birth, head trauma, vitamin A toxicity, separated or malformed sutures, application of pressure, or rare congenital conditions can cause indentations in the skull, according to Healthline. When one of the skull's bones cracks, the depressed skull fracture sometimes dents inward, according to Drugs.com.
As children develop, the six bony plates in the skull normally fuse together to form a suture, strong and flexible tissues, at the edges of the plates, according to Healthline. In rare cases, the sutures separate, causing large gaps in the skull that sometimes form an indentation or bulging area, most notably on the top of the head. Hypervitaminosis A is toxic levels of vitamin A that in children and infants can cause softening of the skull bone and bulging of the soft spot at the top of the head.
Positional plagiocephaly, prolonged pressure to the skull while in the uterus or during birth, is the most common cause of skull deformities in children, according to the Craniofacial Center. A less common cause of dents and bulges in the skull is craniosynostosis, in which one or more of the cranial sutures prematurely fuses together. Though the sutures that connect the skull bones cannot be pulled apart once formed, injury or trauma can cause misalignment of the cranial plates, leading to indentations and bumps in the skull, notes Van Family Chiropractic and Wellness Center.