Anonymous pulse checks give answers but don't help since it doesn't point to a specific unhappy employee.
Regular 1:1s are the best way to get honest feedbacks if its not treated as a transactional meeting. It is important to have briefing sessions with managers on how to deal with empathy.
Mentorship programme - where the mentor is not the manager, is also a great platform for employees to open up and express themselves.
Some of the major indicators are - Not participating in org-wide meetings, frequent absence, Not feeling appreciated/recognized, Not satisfied with remuneration/benefits.
Solving for these will eliminate repeated instances.
In some cases, it is better to let go of the employee to avoid the spread of negativity.