The lawsuit alleges that Brigham and Women's was aware of the "problems with management and conditions" at the morgue even before Everleigh went missing.
Dr Sunil Eappen, the hospital's chief medical officer, said in a statement that while he cannot comment on the specifics of the case, he sympathises with the family.
"We continue to express our deepest sympathies and most sincere apologies to the Ross and McCarthy family for their loss and the heartbreaking circumstances surrounding it," he said.
"As with any instance in which there is a concern raised related to our standard of care or practice, we readily and transparently shared the details with the patient's family."
Henning said McCarthy, 37, and Ross, 36, who have been in a committed relationship for years and were engaged in 2019, were "thrilled" when they found out on February 20, 2020, that Ross was pregnant after multiple attempts to have a child.
Everleigh was delivered prematurely on July 25, 2020, weighing 2 pounds, 5 ounces (1kg). She "suffered medical complications" and was transferred to intensive care.
Her parents held Everleigh for the first time on August 1, read to her, maintained a constant vigil, and had her baptised before she died in her mother's arms on August 6, 2020.
Her swaddled body was transferred to the hospital morgue to give Ross and McCarthy a few days to make funeral arrangements. But, according to the suit, a hospital employee placed the baby on a table that was "not the appropriate or the designated place for the delivery of infant remains to the morgue", because another worker was blocking the racks designed for children.
Apparently, no one knew the baby was missing until August 10 when a funeral home representative arrived at the hospital to pick up the body. Everleigh could not be found.
Her parents contacted Boston police on August 11, who investigated and determined, through video surveillance and employee interviews, that Everleigh was likely thrown away with soiled linens from the morgue on August 7.
Police traced where the body might have ended up, and on two occasions police investigators, as well as trash company workers, sifted through mountains of medical debris often covered in blood and human waste to find Everleigh, to no avail.
McCarthy and Ross are faithful Catholics and wanted a proper funeral and burial for their daughter so they always had a place they could visit her, Henning said.
Now all they have is a box containing a few photos, baptismal water, handprints, footprints and a knit hat.