In the book:
1) the major plot in the book where the President and his National Security Advisor's affair affect his judgment;
2) the National Security Advisor's and the President's collusion to deny Ryan credit for the breakthrough for Middle East Peace.
These are just some of the inconsistencies. Clancy, who is credited as Executive Producer for the movie, has sold out and/or is just too tired any more.
There are lots of authors out there who used to write excellent books, but are now turning out what are in effect only "draft screenplays" and the publishers are marketing these based on the authors' names. Stuart Woods is one currently active. Past ones include Alistair McClain. Now I fear Clancy is in that category as well.
Whoops
I think I saw an interview with him, back after Clear and Present Danger came out, that backed this up. The impression I got was that he couldn't afford to buy back the rights, but he wasn't exactly happy with the way his stuff was being rewritten on the fly by the screenwriters. And that's why he wasn't doing promotions or endorsements for the flicks, and so forth.