Doctors felt their concerns about ventilation and water at Scotland's largest hospital were not addressed, a new report has found.
It was one of a number of failings found by the oversight board for the Queen Elizabeth University in Glasgow, after deaths were linked to infections.
The interim report also highlighted issues with infection prevention and control, and communication.
The health board has apologised for "distress caused to families affected".
Hospital report says failures 'did not cause avoidable deaths' Prosecutors consider Glasgow HSE hospital infection report The oversight board was set up to address infection prevention and control at the £842m facility, which opened in 2015.
A separate independent review was ordered by Health Secretary Jeane Freeman following the deaths of three patients between December 2018 and February 2019.
A 10-year-old boy and 73-year-old woman who died at the Govan hospital were found to have contracted Cryptococcus fungal infection which can be linked to pigeon droppings.
A third death, involving a 63-year-old patient who contracted the fungal infection Mucor, was also investigated but no link was found.
Millie Main, 10, died in 2017 from an infection, which her mother believes was "100%" due to contaminated water.
Clinicians' concerns The oversight board recognised "significant shortcomings" in the construction and handover of the QEUH, as well as how NHS Greater Glasgow and Clyde (NHSGGC) responded to emerging and related problems.
In a report published on Monday, the board said that clinicians had raised concerns about water and ventilation but did not feel they were being addressed.
It also said there were shortcomings over how "'warning signals' about potential problems were - or were not - acted upon over the years".
On the issue of infection prevention and control in the health board, the report said that national standards had been "translated through a profusion of local guidance" - meaning there was a risk of promoting a Glasgow "way of doing things".
'Kept in the dark' The health board was placed in level four special measures by the Scottish government last year amid the ongoing concerns.
Wards 2A and 2B at RHC were closed in September 2018 after contamination was found in water outlets and drains in 2A, and children were moved to wards in the main QEUH building. pg