losing prisoners
You can lose prisoners for the simple reason prisons must release them unless there is legal authority to hold them (prison governors can be charged with unlawful imprisonment just like anybody else and it carries a very heavy sentence). So if HO fails to provide said authority for a foreign prisoner - they go free.
Needless to say, it would be wrong to dignify the way HO track these matters with the title "system", as any judge or prison governor can confirm. That's before you start on trivia like they have British spouses and small kids