I am afraid I am not able to reproduce your issue.
I just launched a new WordPress Multisite, configured it to use subdirectories instead of subdomains as explained here and configure the main domain name by executing the following command in the server:
sudo /opt/bitnami/apps/wordpress/bnconfig --machine_hostname mydomain.com
After that, I created a couple of subsites, a couple of categories and a couple of post and I can access to the categories page, click on them, etc.
Can you check if you have applied the same configuration I did? In particular, the domain name configuration using the bnconfig tool.