There were naturally occurring gravity wells on Archetryx. (PROSE: The Apocalypse Element)
On Mars, a decaying segment of the Key to Time was disguised as the capstone of a pyramid. When Zara converted it to its true form, a gravity well was created that caused earthquakes and hurricanes for three decades. This devastated the civilisation of the Ice Warriors. (AUDIO: The Judgement of Isskar)
The pages of River Song's diary were soaked in the gravity wells at the end of time. (AUDIO: Friend of the Family)
Dalek installations had artificial gravity wells to allow for quick vertical transport. (TV: Planet of the Daleks, AUDIO: The Triumph of Davros)
After Donna Noble retconned the word "Gravity" into "Mavity" during a brief encounter with Isaac Newton, she failed to understand the term "gravity well" when the Fourteenth Doctor observed that a corpse was stuck in the gravity well of a spaceship, causing him to instead say "mavity well". (TV: Wild Blue Yonder [+]Russell T Davies, Doctor Who 60th Anniversary Specials (BBC One and Disney+, 2023).)