Typos in the email. If a guest mistypes their email they will not get the confirmation or updates. Call them on the phone number, or use OTP Verification at checkout to confirm the email or phone before ordering.
Same person, many guest orders. Each guest order stands alone. You will see the same email on several orders, but there is no single customer record until they register.
Guest registers later. Their old guest orders stay as guest orders; they are not moved into the new account.
Reward points and wallet. Not available to guests. If you run a rewards programme, invite guests to create an account after the order.
Customer-group prices. Special prices for a customer group (wholesale, VIP) need the shopper to be logged in. Guests see normal prices.
Fake COD orders. Guest checkout makes ordering easy for everyone, including pranksters. Limit COD with Payment Restrictions and require phone.
Guest checkout cannot be switched off from the admin. The switch is missing from the Checkout settings today.