This is solved by ourselves whereby we found that some URLs were being handled by facetapi_pretty_paths when in fact they were URL redirects defined by us.
The simple solution was to ensure that the redirect module weighting was lower than facetapi_pretty_paths so that redirect executed first to process the URLs that had been defined as redirects. Any other URLs not defined as redirects could pass through and be handled by facetapi_pretty_paths
The redirect module weighting was adjusted from 0 to -1 and the facetapi_pretty_paths weighting left unchanged at 0. Based on general instructions at: https://www.drupal.org/docs/7/creating-custom-modules/howtos/how-to-upda...
The weighting was adjusted by altering the system table in the site's MySQL database, changing the weight column values as described above for the modules. It is also possible to use https://www.drupal.org/project/modules_weight but we adjusted the table in our initial testing. We will use a update_hook containing the same database operation when rolling out to production.
Ideally what my colleague Sam was looking for was to be able to restrict facetapi_pretty_paths to a specific base sub URL, so that any other URLs without this pattern would be ignored by facetapi_pretty_paths - raised an issue for this https://www.drupal.org/node/2900582
Also saw https://www.drupal.org/node/2889812 which might be an alternative implementation.
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