Primarily, the Spider called the Fly ‘witty’ to flatter and seduce the Fly whom he actually thought ‘silly’. But I think, the way the Fly replies to the initial invitations and offerings of the Spider shows her wit.

When the Spider invites her up the winding stairs, into his parlour, she answers that she knows whoever goes up the winding stair, never comes down again. When the Spider offers her some rest upon his little bed, she says that whoever sleeps in his bed, never wakes up again. These replies of the Fly have some touch of wit and intelligence. That is why I think the word ‘witty’ is somewhat fitting for the Fly though the Spider probably did not mean that when he called her so.