There are the only two substantial sections from the TWOK script that are not known to have been shot.
This first one involving Spock mentoring Saavik was possibly not filmed because they wanted to get the story rolling faster.
SAAVIK
He's not what I expected, Sir.
SPOCK
What did you expect, Lieutenant?
SAAVIK
(uncertain)
He's very human.
SPOCK
We can't all be perfect, Saavik.
You must control your prejudices
and remember that as a Vulcan as
well as a Romulan you are forever
a stranger in an alien land.
Around you are humans, and as a
member of the Starfleet you are
unlikely ever to escape their
presence or their influence.
You must learn to tolerance in addition
to all else I have taught you.
Tolerance is logical.
This second bit almost certainly was filmed but it was deleted very early as they rearranged the reveal of when Khan was in command of Reliant till after Chekov contacts Carol.
JOACHIM
Steady on course. All systems normal.
KHAN
It's not much different from
Enterprise.
(beat)
When I was a guest aboard her some
years ago, Captain Kirk kindly allowed
me to memorize her technical manuals.
And now, Mr. Chekov, let us review:
You say you have no details of
Project 'Genesis' ?
CHEKOV
Beyond what I told you, sir, it is
classified information.
KHAN
Umm. And would Admiral Kirk have
access to such information?
CHEKOV
I would think so, sir. He's on the
Fleet General Staff.
KHAN
Then to whom do you report directly
regarding Genesis?
CHEKOV
To Doctor Marcus, the civilian
director of the experiments on Space
Laboratory Regula I.
KHAN
(thinks)
I see. Helmsman?
HELMSMAN
Aye, sir.
JOACHIM
May I speak? We're all with you,
sir, but consider: we are free,
we have a ship and the means to
go where we will. We have
escaped permanent exile on Ceti
Alpha V. You have proved your
superior intellect and defeated
the plans of Admiral Kirk.
You do not need to defeat him
again.
KHAN
He tasks me -- and I'll have him. I'll
chase him round the moons of Nibia
and round the Antares maelstrom and
round perdition's flames before I give
him up.
(as no one speaks)
Prepare to alter course -- for Space
Station Regula I
That's it. If you read the script and see lines you don't recognize it is because they were edited out -- NOT because they were never filmed. Having seen the Director's Cut and the UCLA rough cut I can vouch for all the rest being shot. The only exception I can't vouch for is the very end of the movie after Spock leaves the bridge to fix the engines. The rough cut at UCLA does not contain that portion of the movie.