Hi @GertJ 
I tried to reproduce your issue but without success. Packages was updated correctly.
Here is my STR:
- install percona-toolkit 3.0.13
 
- check version
 
- execute yum update percona-toolkit
 
- check version
 
[vagrant@localhost ~]$ pt-show-grants --version
pt-show-grants 3.0.13
[vagrant@localhost ~]$ sudo yum update percona-toolkit
Failed to set locale, defaulting to C
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: 
mirror.mirohost.net * extras: 
mirror.mirohost.net * updates: 
mirror.mirohost.netpercona-release-noarch                                                                                          | 2.9 kB  00:00:00      
percona-release-x86_64                                                                                          | 2.9 kB  00:00:00      
(1/2): percona-release-noarch/7/primary_db                                                                      |  23 kB  00:00:00      
(2/2): percona-release-x86_64/7/primary_db                                                                      | 1.1 MB  00:00:00      
Resolving Dependencies
–> Running transaction check
—> Package percona-toolkit.x86_64 0:3.0.13-1.el7 will be updated
—> Package percona-toolkit.x86_64 0:3.2.0-1.el7 will be an update
–> Finished Dependency Resolution
Dependencies Resolved
=======================================================================================================================================
 Package                          Arch                    Version                        Repository                               Size
=======================================================================================================================================
Updating:
 percona-toolkit                  x86_64                  3.2.0-1.el7                    percona-release-x86_64                   12 M
Transaction Summary
=======================================================================================================================================
Upgrade  1 Package
Total download size: 12 M
Is this ok [y/d/N]: y
Downloading packages:
No Presto metadata available for percona-release-x86_64
warning: /var/cache/yum/x86_64/7/percona-release-x86_64/packages/percona-toolkit-3.2.0-1.el7.x86_64.rpm: Header V4 RSA/SHA256 Signature
, key ID 8507efa5: NOKEY
Public key for percona-toolkit-3.2.0-1.el7.x86_64.rpm is not installed
percona-toolkit-3.2.0-1.el7.x86_64.rpm                                                                          |  12 MB  00:00:03      
Retrieving key from file:///etc/pki/rpm-gpg/PERCONA-PACKAGING-KEY
Importing GPG key 0x8507EFA5:
 Userid     : “Percona MySQL Development Team (Packaging key) <mysql-dev@percona.com>”
 Fingerprint: 4d1b b29d 63d9 8e42 2b21 13b1 9334 a25f 8507 efa5
 Package    : percona-release-1.0-21.noarch (installed)
 From       : /etc/pki/rpm-gpg/PERCONA-PACKAGING-KEY
Is this ok [y/N]: y
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
  Updating   : percona-toolkit-3.2.0-1.el7.x86_64                                                                                  1/2  
  Cleanup    : percona-toolkit-3.0.13-1.el7.x86_64                                                                                 2/2  
  Verifying  : percona-toolkit-3.2.0-1.el7.x86_64                                                                                  1/2  
  Verifying  : percona-toolkit-3.0.13-1.el7.x86_64                                                                                 2/2  
Updated:
  percona-toolkit.x86_64 0:3.2.0-1.el7                                                                                                  
Complete!
[vagrant@localhost ~]$ pt-show-grants --version        
pt-show-grants 3.2.0
Most probably you didn’t have enable percona repository and that is why there weren’t any available updates.
In order to enable our repository it is needed to install percona-release package and enable needed repository using percona-release script. 
You can find more info here: 
https://www.percona.com/doc/percona-repo-config/percona-release.html