Employer deducted cycle scheme after tax

Spoon

I'm enrolled in CycleScheme and recently noticed that my employer had deducted my CycleScheme payments AFTER my tax, NI, pension and student loan, instead of deducting it from my gross pay, as it's designed to be. This resulted in my monthly salary being down for a couple of months due to the deduction being made in the wrong place. I raised this with HR who worked out how much I was down by, but refused to just give me a one-off payment for the amount. Instead I had to wait until the following month and they put it in with this month's pay. However, as I was then taxed etc on the amount again, I've ended up with only 2/3 of the money they owed me. What can I do? I've received less pay due to an HR error through no fault of my own. Our HR manager doesn't know how to fix it and so has ended up telling me it's too much hassle working out a way to pay it to me. Do I just have to let it go? The same has happened to other employees with the scheme in place, but HR have kept quiet and not owned up to the error apart from in my case where I raised it with them.