I have been noticing this happen occasionally; I'll see a random point/vertex detached or close to my mesh that is connected to the mesh(far left orange dot). If I delete it, it will erase my mesh and if I want to manipulate the object, it totally starts to deform/mess with it as shown below. Anyone else have this issue/ know why this is happening? It's probably a newbie mistake but can't seem to understand. Thank you!
Isn't it the origin of your mesh?
If you want to put it in the centre of your mesh, in Object Mode press Ctrl + Shift + Alt + C and select Origin to Geometry.