Why is my scaling (Ctrl-A) causing me problems?

I'm working on a human character and I'm in the middle of modeling.

I have the entire body near complete but I noticed some of my points were off. Like the chest-shoulder region wasn't matching up. I tried to grab with G but that ruined the placement of my character hips. So i tried to scale it, same issue.

I decided to move the points to where I needed them the attempted to adjust the hips. Now when I move or scale the hips, my previous points are not set off again. Can someone tell me what my issue is??

I have Mirror, Skin and Subsurf modifiers added, in that order, but not yet applied.

• It would be good if some screenshots were added, where mesh is shown before and after grabbing. You could also include modifiers' options there – Mr Zak Aug 6 '15 at 14:16
• And are you scaling the mesh / its parts with S ? Or apply scale with Ctrl+A ? – Mr Zak Aug 6 '15 at 14:19
• If images aren't working for you, try pasteall for images or blend files. – Dr. Who Aug 6 '15 at 14:24
• Mac or Windows? – Dr. Who Aug 6 '15 at 14:31
• Try pressing 'o' to turn off proportional editing. – Dr. Who Aug 6 '15 at 14:36