The second referendum amendment put forward by the Scotch was defeated largely by Labour's abstention... the Kyle-Wilson motion will be the real vote, erm. There are still a number of mechanisms available to facilitate a third (and not necessarily final) vote on May's deal. The house could overrule the speaker or HRH could be called upon to start a new session of parliament. I'd say whoever fills Sir Humphrey's shoes in the real world arena of today panicked a bit thinking the third vote might pass hence the speaker's intervention.