In that case, it appears to have been a mistake. Your brother's GF can countersign your application, but you cannot countersign her application.
This is from the official HM Passport Office guidance for their staff:
3.5 Referee: related to the customer
The person confirming identity must declare their relationship to the customer, and some may tell us they are related to the customer.
You must always call the referee, before you reject them, if it is unclear if they are related to the customer.
Friends, family friends or a relative’s friend or partner (for example, cousin’s partner) can be accepted. If the person has described their relationship as ‘godparent’, for example, you can accept them if they are not related (a close family member).
You must not accept a referee if they are related to the customer, for example by birth, marriage or civil partnership, divorce, or adoption. You must reject them if they are:
- a relative or member of their close family (for example, siblings, in laws, cousins, step-parents)
- a relative of their partners family (for example, siblings, cousins, step-parents)
- in a relationship or partnership similar to marriage (for example partners, whether or not they live together)
Source:
https://www.gov.uk/government/publications/confirming-identity-countersignatory-and-digital-referees/confirming-id-referees
In this case she would be a "relative’s friend or partner (for example, cousin’s partner) can be accepted." in particular here, brother's partner.
Perhaps they mixed things up? She can countersign your application because it is ok if you are a relative of her unmarried partner. However, you cannot countersign her application because you are related to her partner (your brother).