Firstly, the employer most definitely hasn't committed theft. The Theft Act 1968 states:
"A person’s appropriation of property belonging to another is not to be regarded as dishonest . . .if he appropriates the property in the belief that he has in law the right to deprive the other of it, on behalf of himself or of a third person"
and
" “Property” includes money . . . "
So the matter is purely a civil one, not a criminal one. If they've definitely overpaid you they have every right to take the money. If they've not overpaid you then, clearly, they haven't. If you can't agree on the matter then only a court can decide the issue. If you're confident that you can show that you weren't overpaid, initiate court action through the official online procedure here:
https://www.moneyclaim.gov.uk/web/mcol/welcome
Chris