That doesn't sound like a flaw, but eagle moss specific design. Unlike the real studio model they altered the angles of the lower pylons to allow for a sturdy support system. And it is distracting.
Yeah, it's my most hated change so far. To alter the dimensions just to (supposedly) make it sit easier is a terrible call, in my opinion. DS9 is the only one I don't have on display, instead I have all the ships around my Playmates DS9.