If you do a search with a join of a JQL search and a core.issues table or two JQL searches and try to join them (and they have overlapping column names) it will return the first column of that only. For example:
select jql.ID, CI.ID
from table(AUX.JQL('ID,issuekey,', 'type = bug')) jql
join core.issuelinks CIL on CIL.destination = jql.ID
join core.issues CI on CI.ID = CIL.source
jql.ID and CI.ID will return the same column where CI.ID should be the source ID.
As a workaround use aliasing:
select jql.ID as jqlid, CI.ID
from table(AUX.JQL('ID,issuekey,', 'type = bug')) jql
join core.issuelinks CIL on CIL.destination = jql.ID
join core.issues CI on CI.ID = CIL.source