A stack trace will include all of the function calls leading up to the error, which is why it is helpful for debugging. You can see an example of what one looks like here:
If you can share the stack trace, this will help us to identify the error.
There really is no such thing as a “standard” configuration. Every server has a specific combination of Apache version, PHP version, Database server, and OS version. This specific combination is important for us to know when a bug is found. For example, I’m not able to reproduce this under Red Hat Enterprise Linux Server release 7.6 (Maipo) with Apache 2.4.6, PHP 7.2.14, and the mysqli driver against Ver 15.1 Distrib 5.5.60-MariaDB.
Can you share a link to “OJS3 cookies bug”? Note that only the “Expire User Sessions” option under the Administration menu relates to OJS cookies. Does the problem resolve if you only Expire User Sessions and do not run the Clear Data Cache and Clear Template Cache options?