It does seem like they had a few minor issues rather than systematic abuse. I suspect HMRC wanted a few juicy headlines to set an example to the lower profile employers.
My understanding is they were in the wrong because they advanced money to apprentices to buy discounted knives, for accomodation deposits and for one to have their car fixed and then the loan deductions meant the take home was below minimum rates.
They also were late moving a few workers to higher wages when they had birthdays - as minimum wage is determined by age - under 18, 18 to 25 and over 25.
That said loans against future earnings etc are a tricky area as they are often the way “slave labour” employers hook in staff i.e. loan a large amount upfront for travel, or deduct a lot for accomodation meaning the take home is negligible and the worker is trapped.
Northcote were not doing this but I can understand why the law is fairly prescriptive in this area and thus catches the well intended as much as the rogues.
The solution to not falling foul of changes in age related minimum wage rates when people have birthdays is to pay sufficiently above the minimum to start with. Then a birthday doesn’t usually matter.