It's not Elise that is causing the damage. It is her Spiderlings.

Similar, but different.

most champion have just 1 minion, elise has 3 + herself she already hits like a ***** one her own if you added the A Shred % to her minions shes get max reduc after only 1sec with Frenzy its due to balancing her out, and the reason why in Human form her exploding spider procs is because it's nt a minion its a spell cast... she sends a spier out and it explodes, it dosnt att you and it isnt like a minion it cant be directed towords a champion. therefore theres not an issue the issue is she has multiple minions at her disposel in Spider form.

Spiderlings deal physical damage and take reduced damage from multi-target abilities.

From the wiki.

This seems like a bug, Yorick ghouls' autoattacks proc black cleaver and they do physical damage, no reason Spiderlings shouldn't.