The autofill feature does not ever add new accounts by itself, so you will have to provide more information about what actions you’ve taken if you want an answer.
It looks to me that you created two passkeys for the Kraken site (at least one of them on Oct. 10, as shown in your first screenshot), and that the Bitwarden browser extension could not find your existing Kraken accounts at that time (because your password manager account did not have access to your “top secret” collections as of Oct. 13). Thus, the October 10 passkey was saved in a new vault item. When you created the second passkey, there may have been an option to overwrite the first passkey (which you may have elected not to do), or the option may not have presented itself if the two URLs were sufficiently different.
It’s unclear why there is an “Unable to Sign in” error message in your second screenshot, but perhaps you’ve autofilled your Kraken Pro credentials on the Kraken site (or vice versa).
Autofill does use your “original accounts” (now that you’ve granted permission to access the “top secret” collection). Autofill will also try to use your two new vault items (with the passkeys); if you want to prevent this, you’d have to delete the “Website (URI)” strings from those items, or set the URI match detection method for those URIs to “Never”.
Are you perhaps trying to ask something different — e.g., how to move the newly created passkeys into the original “top secret” vault items? It is not possible to move passkeys from one vault item to another, so you’d either have to copy the username/password (and other) information from the original items into the items that have the passkeys, or delete the passkeys (they must be deleted both on Kraken’s server and in your Bitwarden vault) and create new passkeys to be stored in your original login items.