I recently joined a new company and am trying to make sense of their JIRA queue. If I look at the issues under the project they vary from the issues listed under the project backlog. Why would there be a difference between the two? What is the best way to align them?
Assuming that your company is using Jira Agile, your project backlog is defined by a Board, defined by some criteria: typically either a project or a search query. That search query may be a subset of the project or may even incorporate issues from other projects.
If you have the appropriate permissions, you can see the query by going to Board -> Configure from the top-right hand corner of the screen. On the General tab, you can find the Saved Filter configuration that defines the board.
You can configure the Saved Filter to pull from the entire project, or refine the query as needed by writing your own query in Search, and saving it as a Filter. Make sure to share the filter with the project so that others can see it.
Firstly you need to find out from the Project Manager how JIRA has been configured for this project. You have mentioned 1) Issues under the project 2) Issues in the backlog.
1) I interpret project issues as those traditionally tracked in a RAID log by a PM. Confirm with your PM if this is what project issues actually are. JIRA is highly configurable, so without knowing how it has been set up including usage of labels, you won't be able to solve your problem.
2) Issues in the backlog should be Epics or User Stories. Confirm with your scrum team if this is definitely the case.
JIRA is powerful, but sometimes without standardisation of usage across an organisation you can see some real turkeys. A mess basically.
If you have not already done so, set up your own filters and dashboards to interrogate the issues under the project. Confirm with the PM and scrum team how labels are being used. Then look out for issues that have labels which should be mutually exclusive.
Once you have gone through the above process you may be able to confirm exactly what is going on.