There's no perfect way of syncing UTXO blockchains, as whether some withdrawals/deposits should be merged or not depends on where they are sent and whether recipient addresses belong to one wallet or not.

We do allow adding multiple xpub keys to one Koinly wallet (separating them with a comma) which should help mitigate most of the issues like this.

But some transactions may still need manual fixes, especially if multiple outputs were split into multiple inputs to non-related wallets.