Symptoms

Some issues are missing from plan or work mode and the filter shown up the missing issues correctly under issue navigator.

Diagnosis

1. Check mapping of the columns
2. Check the issues whether it is returned using the filter(Agile > Tools > Filter > View in Issue Navigator)
3. Check any quick filters has been toggle on which affect the search result
4. Check any filter on the swimlanes which based on the queries

Cause

The query size limit under JIRA Agile Configuration has set a limit and no message being shown to notify the user. Further information can review on bug ticket created:
  GHS-5938 - Getting issue details... STATUS

Workaround

1. Go to "Administration" > "JIRA Agile" > "JIRA Agile Configuration"  in JIRA
2. Look for the Query Result Limit.
3. Set it to Never Ask or set the limit to a higher number