The Most Common Mistakes Employers Make with Medical Leaves and How to Avoid Them

Managing medical leaves of absence should be straightforward, yet even well-intentioned employers stumble into compliance traps that create unnecessary risk. Between FMLA, ADA, PTO policies, state leave laws, and internal procedures, it’s no surprise supervisors often feel overwhelmed. But the good news? Most mistakes are completely avoidable with some structure, awareness, and communication.

Below are some of the most common pitfalls I see employers run into and what to do instead.

Letting Employees “Opt Out” of FMLA and Just Using PTO Instead

One of the biggest and most misunderstood pitfalls is allowing an employee to decline FMLA when they should be on protected leave.

Employers often think they’re doing the employee a favor: “Do you want to use your PTO instead of going on FMLA?” “Do you want to save your leave?” Or worse, simply not designating FMLA at all and letting the employee burn PTO or take time off informally.

Here’s the problem: FMLA designation is the employer’s responsibility, not the employee’s choice. When you fail to designate leave properly, you risk:

• Violating the employee’s right to job protection

• Creating inconsistent or unfair practices

• Complicating attendance and return-to-work decisions

• Triggering interference claims

Even if an employee wants to use PTO instead of FMLA, you must run FMLA concurrently if they meet the eligibility and qualifying conditions. PTO can supplement the leave, but it can’t replace it.

The fix: Create a clear, consistent process for evaluating every medical-related absence for FMLA eligibility and train supervisors to notify HR immediately when an employee mentions a medical condition.

Not Recognizing When an Absence May Be FMLA-Qualifying

Employees rarely say:

“Hello, I would like to formally request a leave of absence under the Family and Medical Leave Act.”

Instead, they say things like:

• “I’m having surgery.”

• “My doctor wants me out for a few weeks.”

• “I need time to care for my mom.”

• “I’ve been in the ER twice this month.”

If supervisors aren’t trained to recognize these cues, qualifying leaves get missed and that’s an easy way to land in compliance trouble.

The fix: Implement a “trigger word” process and ensure frontline leaders know when to escalate to HR.

Letting Supervisors Handle (or Hide) Leave Issues on Their Own

Supervisors sometimes try to “manage around” an employee’s situation to be helpful or avoid paperwork. But when leaders approve long absences without involving HR, they inadvertently open the company to risk.

This can result in:

• Inconsistent treatment between employees

• Missed FMLA deadlines

• ADA accommodation issues

• Unclear documentation

The fix: Create a culture and standardized procedure where all leave-related conversations are routed to HR with no exceptions.

Assuming FMLA Is the Only Law That Applies

Even when FMLA is properly handled, employers often overlook other overlapping obligations, such as:

• The ADA (reasonable accommodation and extended leave)

• State family and medical leave programs

• Pregnancy accommodations

• Workers’ compensation leave requirements

• Company-specific leave policies

When employers treat leave as a one-track process, they may shorten leave prematurely or deny reasonable accommodations.

The fix: Evaluate every leave situation through multiple lenses and document how decisions are made.

Cutting Off Communication During the Leave

Some employers worry that reaching out to employees during medical leave could be seen as intrusive. While boundaries matter, radio silence creates anxiety and leads to unclear return-to-work expectations.

Employees benefit from check-ins, and employers need updates to plan staffing.

The fix: HR should schedule periodic, supportive touchpoints not to pressure, but to clarify expectations, share resources, and discuss any anticipated changes. Direct managers should not reach out to employees in order to avoid any perception that the employee is being asked or coerced to work or return early.

Mishandling Return-to-Work and Fitness-for-Duty Processes

A few common issues:

• Requiring unnecessary medical details

• Accepting vague return-to-work notes

• Not evaluating whether restrictions trigger ADA obligations

• Allowing employees to return to “full duty” when that’s not accurate

• Forgetting to reinstate benefits or status

Return-to-work is a critical compliance moment and mistakes here often undo months of proper leave management.

The fix: Use a standardized return-to-work procedure and treat restrictions as a cue to begin the ADA interactive process. Do not automatically deny an extension of leave without completing an interactive process.

Final Thoughts: Clarity, Consistency, and Compassion Win Every Time

Medical leaves are stressful for employees, supervisors, and HR alike. But most pitfalls stem from a lack of process not malice or intent.

When employers establish clear workflows, train supervisors, and approach leave situations with empathy and consistency, they dramatically reduce compliance risk and build trust with their teams.

If you’d like help tightening up your leave policies, training managers, or conducting a risk review, Freestyle HR is here to support you. We can provide fully outsourced leave management from first request to return to work, or provide you with a toolkit and training to manage leave on your own.