On closer inspection, it looks like the lower flange (the one that is separating) is not meshing node-to-node with the web, which the top flange is. Any thoughts on enforcing compatible meshing along that interface? One idea would be to construct the I-beam of two C-channels back-to-back, but that seems like a pain.
How do you structural guys handle this?
The mesh is incompatible unless you have edges that line up or you add splits. This will allow the global bonded contact to 'merge' the nodes. Add contact constraints manually and it should fix your problems. Additionally you wouldn't use thick shells for beam members.