Thanks for your post. I suspect the symbols in question have been moved off-grid somehow, perhaps using the Arrange | Align to Grid command (it looks like the Tops of the symbols have been aligned to the grid).
In any circumstances where symbols have lost their alignment to the grid, select the symbol(s), rightclick and choose Align Origins to Grid. This works on single symbols and multiple selections alike and moves the symbol so that its origin (insertion point) sits on the nearest gridpoint and all IOs will also be on gridpoints..
I hope this is helpful.