This solution is based on Rik Wisselink's suggestion in the comments under the quesiton.
The idea is to find objects within the GUI whose positions are outside of the GUI frame. The code below should be run from within the GUI within any callback function or at the end of the initializer function and requires the 'handles' vector which is a structure listing all handles within the GUI.
handleVec = struct2array(handles);
positions = get(handleVec, 'Position');
xPos = cellfun(@(x)x(1), positions);
yPos = cellfun(@(x)x(2), positions);
isout = xPos > 0.99 | yPos > 0.99;
The next step depends on how many objects you have to move. If it's just a few, it might be best to just get the names of each object and then make the adjustments from within guide. If there are lots of objects, you'll need to manually place each of them from within the initializer function.