As part of our R&D workflow, I've prompted up questionnaire as a jira few custom field in one screen when transitioning from one status to another. I want to be able to track all tickets that marked as 'No' on one of these custom fields in the popup - this data appears in the history of the ticket
If I understand you correctly, you are setting a custom field in response to some questions on a transition.
You could create a JQL filter for the issue that have the value you care about (e.g. "No" in the custom field), save the filter, and subscribe to it to receive schedule notices of the issues.
If you instead want more immediate information, you could use an automation rule to watch for changes to the custom field and to notify you and/or other people.
Just to confirm, did you add a custom field first in order to set it during the transition?
If so, you should be able to query it with JQL, according to these two defects that were fixed a while ago:
If you cannot query the field, you may want to submit a defect to Atlassian support. You should be able to do that as the site admin for a paid instance of Jira: https://support.atlassian.com/contact/?postauth=true#/
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