That was Electrum's precaution to prevent unconfirmed dust outputs to be spent with your other UTXO in case it has a chain of unconfirmed parents or very low fee.
That makes sense 
At least I could overwrite it.Electrum should do the same for any small input that isn't worth the fee it takes to send it at that moment. I still see transactions with dust inputs that add more to the total transaction fee than their value. So without those inputs, the transaction would be smaller and the user would spend less.