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! 
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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.
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$\begingroup$ I did that already, that vertex just sits there... maybe earlier in the process it was misplaced? $\endgroup$– NoelleCommented Jul 9, 2018 at 10:10
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$\begingroup$ yes I think that it's the origin of your object, you could not see a unique vertice in Object mode. If you go in Edit mode and select all (A) you won't see any vertice at this place. If your origin is placed here and stays here when you do an Origin to Geometry it means that there is another vertice far away that makes the centre of your mesh there and not in the main mesh. So when you're in Edit mode and make a select all you should be able to see that isolated vertice $\endgroup$ Commented Jul 9, 2018 at 11:02