For the first 3 months of your sister's SWA claim, the claim should have been categorised as Nil Income, for the remainder of her SWA claim, it should have been categorised as Pending One Parent Family Payment. If this wasn't done, it may have been the reason for the incorrect calculation of arrears.
Another piece of info for you - although the different scheme sections talk about payments and refunds, no actual monies change hands between HSE and SW (i.e. the CWO doesn't actually see a cheque from SW for any refund!). Recoupment between schemes is an accounting exercise between the different "pots" in DSFA.