The folk etymology is possibly related to acne, where the head of the pimple forms after something bad has been going on beneath the surface.
to come to a head
- idiom To rapidly come to a turning point.
#:The escalating crisis between England and her American colonies came to a head when fighting broke out in 1775.
- idiom To suddenly reveal that which has lain latent for a time.
#:His festering anger came to a head after the incident.
- idiom To suddenly make mature or perfected that which was inchoate or imperfectly formed.