To actually find out why this is happening so you get a better idea of how to fix it, run a drush command with the --debug option. eg: drush pm-list --debug. Then look through the output to see anything that might be causing the problem.
http://blog.2pha.com/fixing-drush-needs-higher-bootstrap-level-run

To actually find out why this is happening so you get a better idea of how to fix it, run a drush command with the --debug option. eg: drush pm-list --debug. Then look through the output to see anything that might be causing the problem.
https://2pha.com/blog/fixing-drush-needs-higher-bootstrap-level-run