Hard to know without plans and pictures. Is it even legal? You say loft conversion so I assume you are not in the states, here ceiling have to be at least 7’ tall in the majority of the space

Plans all been checked and rubber-stamped by the council. It's the door to the ensuite.

You have to show us more ...

Sorry your picture doesn’t explain your question.

Did you mean to type "Trying to put the top door facing in but not enough room as the ceiling is so low " ?

Can the door open out?

Yes partim. The door opens in the way.

in the way of what?

Post a picture of at least the wall where this is going.

Based on the photos, I'd say shortening the door would solve the problem.

If the door has room to open out, just do that.