The child was found dead in March 2013, and while a coroner's report did not determine a cause of death, it did find that Isabella had fractures in her left arm and bruises on her arms, legs and face.
Now, her mother Sara Jane Wiens, is demanding answers and has filed a suit two years later.
Wiens says the ministry took her daughter away when she was two months old as they ruled she was unfit. (She has a learning disability).
"They're telling me I can't parent and that I'm dangerous and that I will potentially harm my child and ... then they take her from me, put her in a home and she ends up dead," she said.
But when Wiens raised concerns about her daughter's well-being during supervised visits, she says she was ignored.
"I saw bruises and constant diaper rash, and I brought these things up but they disregarded them," Wiens said.
Then, in March 16 2013, police and family services showed up at her door early morning, and told her Isabella had died while in care.
"I ran outside my back door and I screamed bloody murder and I broke down," Wiens said.
When she died a part of me died."
Wiens said she wants the ministry to acknowledge their system did not work for Isabella, and wants an apology.
"I've not been able to get over this ... I've been stuck in limbo for two years," she said.
"There are flaws in the system and they seriously need to be fixed. This is so wrong. No one should have to go through this."
Stephanie Cadieux, the minister of children and family development, said she couldn't get into specifics.
"Short of saying any time a child dies it's a tragedy and I certainly feel for the mother, for her loss, it's incredibly tragic ... I can't speak any more about anything that may or may not be related to the ministry in this circumstance."