Why can't I search for issues for a certain user in the assignee field?

When I search for issues assigned to a specific user, using assignee = x user, no issues pull up even though there are issues assigned to that user. The user was assigned only to subtasks to a parent issue. I could however find the user if I put assignee WAS x user. I tried searching for other users and some user's issues would pull up and others would not by using assignee = y user. Some users assigned to subtasks would show up too.

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That sounds correct.  If you use "assignee = X", it looks for issues that currently have that person as the assignee.

If there are definitely issues with them as the assignee, then check the rest of your query to see if they are excluded for another reason (searching the wrong project, issuetype, custom field etc).  If you still have an issue, then it might be a damaged index, but I would post your actual JQL here first to see if we can spot anything wrong with it.

project = PI AND issuetype in subTaskIssueTypes() AND assignee in (DPeregrina)

The tickets with user's assigned that won't pull in when queried also aren't allowed certain transitions if the transition has a condition of "only assign is allowed to transition".

Ok, that's a nice clear query and a new symptom that could tell us a lot more. Now, we need to find an issue that *should* appear (assignee currently DPeregrina, and it's a subtask in PI) and look at all the user fields on it.

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