I don't see any option in pt-show-grants to do this kind of restriction. There are options for --only and --ignore specific users, but not tables. Nor is there an automatic option to ignore grants on nonexistant tables.
I also glanced in the code, and it doesn't seem to break out the tables to scan through them for any reason.
For what it's worth, I don't see any error when I try to grant to a non-existant table. I tested on Percona Server 5.6.16:
mysql> grant all on test.nonexist to 'user'@'%';
Query OK, 0 rows affected (0.00 sec)
$ pt-show-grants
. . .
GRANT ALL PRIVILEGES ON `test`.`nonexist` TO 'user'@'%';
Can you tell me anything else about your version of MySQL and the specific error that it produces when you try to run that grant script?
Re your comment:
The difference between ALL PRIVILEGES and specific privileges seems to be deliberate, according to Bug #10406 Grant all command does not give error though table does not exist.
If you use GRANT CREATE, SELECT ... ON test.notexist TO 'user'@'%' then this works. As long as you include CREATE privilege, then it permits the grant to the non-existant table.
Anyway, that's interesting trivia, but it doesn't address your original question.
This has been requested before, but never implemented. It was recorded as a "blueprint" (like a feature request) here: https://blueprints.launchpad.net/percona-toolkit/+spec/pt-show-grants-for-nonexistent-tables
Perhaps someone would like to implement a patch and contribute it to Percona Toolkit?