Hi,
Sorry if this is a really stupid question.
To apply for a phd place you need to have a certain grade for your undergrad and get a distinction overall for your masters course. If you are applying for a place but currently doing your masters course you won't know what grade you get until you actually start your phd. If you applied in the last few months you wouldn't even have got your first round of results to get an indication of how well you may do.

I'm sure I must be missing something here!

You should be able to request an official interim transcript from your university/department. Ask your referees to also include what they think you'll get for your masters degree in their references.