A statement from the executive cited "unprecedented demand" at the "extremely busy" centre.
This weekend saw Citywest begin operating as both a walk-in and appointment centre as healthcare workers and the 60-69 age group became eligible for booster vaccines.
The HSE said that due to "a local scheduling error," which they are now examining, people were left to queue for up to five hours. Local access roads also experienced delays.
The scheduling error led to "a number of people being called for vaccination that weren't eligible for vaccination."
"Our Operations Team at Citywest made every effort to lessen the inconvenience and is reviewing operations with a view to improving the flow and throughput at the site," the HSE said.
Anyone who missed their appointment on Saturday due to the error will be contacted directly by the HSE to reschedule a new appointment.
