If Sebastienne Critchley wasn't in the neonatal intensive care unit this December watching over her son, she was likely on the phone with the Phoenix pay centre, trying to figure out when her long list of pay problems would be remedied.

Critchley is one of tens of thousands of federal public servants who've had their pay messed up for months. In her case, she's been both overpaid and then underpaid over the past several months.

And it couldn't have happened at a worse time.

'A stressful situation'

At the end of November, Critchley gave birth to a son eight weeks early.

"Obviously [it's] a stressful situation and a challenge. That's where my focus and attention needs to be, at the NICU," said Critchley from Edmonton.

"So here I am ... on the phone multiple times, trying to track down a record of employment so I can actually have some income."

For Critchley, who works for Service Canada, the pay nightmare started back in April, when she went on medical leave.

The government kept paying Critchley her full salary. By August, the overpayments still hadn't stopped — and when she repeatedly called the pay centre looking for answers, she didn't get any.

"I was hitting four, five, six, seven months of trying and trying and trying to sort this out and pay this money back. The stress level was just skyrocketing," said Critchley, who'd hoped her pay issues would be resolved before she had her baby and started her maternity leave.

Denied employment insurance

The government finally start collecting back its money in November — and then, her baby came early.

After her son was born, Critchley applied for maternity leave benefits, but was denied employment insurance because she hadn't been issued a record of employment. It's something which, by law, should be issued within five business days.

"They're saying it's going to be 20 weeks for the record of employment," said Critchley. "My manager said basically the file had not been handled correctly, [and] that they should have done what's called an interim record of employment."

Critchley said she can't get her maternity leave topped up until she gets her employment insurance.

She said it's all been very frustrating and upsetting.

Critchley is now worried that her pay issues and the aftermath will continue for the next couple of years, since the government isn't going to recover the rest of the money it's owed in overpayments until she returns from maternity leave in the fall of 2017.

"At that point I'll have to have my taxes reassessed, so that'll be a couple of years down the road," said Critchley.

Feds aware of issues

Marie Lemay, deputy minister of Public Services and Procurement Canada, recently told the media her department is aware of the issues.

Marie Lemay, deputy minister of Public Services and Procurement, says the government understands the tax implications created by the Phoenix problems. (CBC)

"As the year-end approaches … they are understandably concerned of the effect of overpayments and ensuring that their T4 actually reflect their actual earnings," said Lemay.

The government said the overpayments made to some public servants are actually not supposed to show up on T4 slips, and should not be counted as income in 2016.

Critchley is also concerned that when the money she's owed is returned next year, she'll be in a higher income tax bracket — which could have an impact on her family collecting the Canada child benefit, a tax-free monthly payment designed to help with the costs of raising children.

The CRA website, however, notes that any pay errors "will have no income tax or government benefit and credit implications in most cases."

Critchley predicts her Phoenix pay and tax headaches will continue long after her baby boy is home from the hospital.

"They're not going to be resolved by December 31, 2017," said Critchley. "Which is absolutely, utterly ridiculous."