Repopulation centers were unofficial prisons for unlucky males.

When Fragile Y Syndrome was identified in the early half of the 21st century, the organization known as Y Control was created in order to combat it.  The initial plan to restore gender balance was to artificially push fetuses to develop as males but, after realizing that these babies were unable to have male offspring, more drastic measures were introduced. Y Control introduced the Carrier Notification Mandate, requiring all physicians who discovered an unregistered male fetus to identify and report the name of the father. 

Then these carriers were found and "enlisted" into the Repopulation Program, colloquially known as "Repop."  Like the rest of Y Control, Repopulation carried out most of its activities behind closed doors so not much information is available. However, the few details that surfaced created controversy. 

Males carrying a stable Y chromosome were essentially taken prisoner, held against their will at breeding centers where they were forced to conceive as many children as possible.  These fetuses are then adjusted to male and most will successfully carry a Y Chromosome.  They are then allegedly released back into the general population, although evidence of this is scarce.  Concerns about the human rights violations occurring at Repop were left largely unvoiced for several reasons. 1) There was no confirmation of the brutality. No proper investigation or announcement of wrong-doing was released. 2) Mounting a campaign against Y Control for proper reforms would have been challenging since most of the population was involved in a day to day struggle to live. 3) Many viewed the program as a necessary evil to save humanity.