Apart from A Stitch In Time, are there any other novels that are considered rare and difficult to get hold of?
The first printing of "Killing Time", because it was quickly replaced by a slightly revised version.
"Vanguard #3: Reap the Whirlwind" is hard to find in MMPB. My local bookshop's restock of that title ended up being print-on-demand trade PBs (with extra-wide gutters).
Every copy of the first printing of "Stargazer: Oblivion" has several pages each with edges of missing text: a printing error. All corrected versions are second-printing or later. PDFs of the affected pages were put up on the Simon & Schuster website for a time.
The trade omnibus "DS9: Mission Gamma: These Haunted Seas" collected the first two MMPB novels ("Twilight" and "This Gray Spirit") in the "Mission Gamma" miniseries, which had fallen out of print and were becoming very hard for fans to find. But then no omnibus ever came out for the next two MMPB novels in that series, "Cathedral" and "Lesser Evil", so they, too, may also be hard to locate.
Several years before Pocket Books took over the Trek books licence from Bantam and Del Rey, they had published a MMPB collection called "Six Science Fiction Plays" (1975). One of the six plays was "The City on the Edge of Forever", the original unrevised teleplay by Harlan Ellison. Perhaps not that rare, but
impossible to find in Australian second hand bookshops (and do you look in the play section, the SF section, the Trek section, or under "E" for editor Roger Elwood?) It was my Holy Grail - until Amazon introduced its keyword-searchable second hand market - and I found a copy for just a few dollars plus airmail postage.

Pocket Books'
"Six Science Fiction Plays" containing "The City on the Edge of Forever" original teleplay by
Ian McLean, on Flickr
Ellison later had a hardcover, slipcase version of his "The City on the Edge of Forever" unrevised teleplay (plus new commentaries) was announced, but Borderland Press (1995) fumbled its distribution.
(Post edited for clarity). A more successful, further revised, trade PB version (and a hardcover?) finally came out a year later from White Wolf Publishing.

Proposed slipcase edition of "The City on the Edge of Forever" by
Ian McLean, on Flickr
There are only 500 copies of the hardcover, slipcased edition of "The Motion Picture" novelization, signed by Gene Roddenberry. This (and the regular hardcover) edition has a dedication page:
"... to Majel".

Star Trek: The Motion Picture slipcase dedication to Majel by
Ian McLean, on Flickr

Star Trek: The Motion Picture slipcase spine by
Ian McLean, on Flickr

Star Trek: The Motion Picture hardcover slipcase edition by
Ian McLean, on Flickr