They swept wrong. You shouldn't attempt to move part of the balance on a paper wallet. You execute a Tx to move the entire balance to a new private key in your hot wallet. Then you spend what you need to and after you can send the remaining funds to a NEW paper wallet.

It's important with paper wallets to know what format the private key is in. I don't like mnemonic seed phrases because not all wallets support them, and they are just a derivation of the private key. What you want to have is the actual private key, base64 encoded. Any wallet app that won't let you import a base64 private key isn't worth using.