Varieties in strength between metals, for example can't be shown in a model. Atoms and molecules are moving constantly, but you can't see that in most models.
The ball and stick model of ionic compounds, although highlights the presence of bonds, exaggerates the distance between the atoms. Others, like the space filling one, don't show the presence of bonding.
In covalent molecular, the lewis dot diagrams don't express the relative attraction of shareed electrons due to electronegativity. The structure sketches, like hydrocarbons, are misleading as most molecular compounds are 3D structures.