A bunion is an inflammation (and subsequent deformation) of the joint where the big toe joins the main part of the foot. They are persistent and often painful. (ref.) It's thought they affect between 23% and 35% of the population. (ref.)
The common deformity of the first ray known as a 'bunion' is a progressive positional deformity which leads to pain from shoe pressure and bio-mechanical malfunction of the first metatarsal phalangeal joint. While the medial bump is widely considered the etiology of pain, malalignment results in progressive joint adaptation and degeneration. The exact bio-mechanical fault and the etiology of the progression of the deformity remain unclear.
Source : Dayton, Paul D. (2017). Evidence-Based Bunion Surgery: A Critical Examination of Current and Emerging Concepts and Techniques.
It's currently thought that there could be a combination of internal and external causes which might contribute to the formation of bunions - including genetic factors, ill-fitting footwear, and rheumatoid arthritis. But, as the quote above states, exact reasons are currently unknown.