Its still showing randomly which is annoying. I think worth to put some braces around these lines to make sure that there is no empty nulls passing so we can handle this gracefully.

Interesting why we would get nulls passed to COMPARE. As you say. This should never happer.
We will need better trapping and logging to be able to investigate it.
We can add some safety checks to prevent this error but this will not fix the problem I guess.

I think where possible we should not let to the situation where the system error occurs by invoking a sys code with invalid argument. I know it might be impossible task but if we limit at least these scenarios where we know about will be easier for user to understand error. This one above for example is very cryptic and doesn't tell you what happened there.

This is new code version can occurs only in SQL when comparing two columns extract from XML.
We could try run nvl on that nvl(s.column_value.getclobval(),empty_clob()) to make sure is always initialised.