Business credit cards usually come as a family. The bank opens a corporate account, then issues a card to each person under it. When you connect the bank, every one of those arrives as a separate account — so one card and one employee look like two debts.
The transactions are not duplicated. Each card really does post its own, and that is worth keeping: it is how you see who spent what. Only the balance is counted twice, because each card reports the family's debt from its own side.
Fixing it
From then on the card keeps its own register, its balance is no longer counted on its own, and it is no longer offered for reconciliation.
Why it is not automatic
Banks differ. Some show only the corporate account and put every card's activity on it. Some show only the individual cards. Some show both. A rule that guessed from the bank's name would be right for one bank and wrong for the next, and being wrong here moves a number on your balance sheet. So the app suggests, and you decide.
Reconciling a family
Reconcile the parent only. The bank issues one statement, on the corporate account, listing every card's activity — so that is the only statement there is to check against. When you reconcile it, the transactions from every card in the family are there waiting.
A child card is not offered for reconciliation because the bank never issued it a statement to reconcile against.
If entries were already posted
If you had already categorised transactions on the card before linking it, those journal entries stay on the ledger account they were posted to. The app tells you how many. They are not moved, because some of them may sit in months you have already closed and filed — and changing a closed month silently is worse than leaving a tidy-up to do deliberately.