The difference between the two is the team level ssh access will grant access to all the repositories within the team, while the repository level ssh access will only grant access to the respective repository. The repository level ssh key will override the team level ssh key if configured on the repository level. Here’s a link to our documentation on how to set it up.
Since this might include sensitive details, for further help with this, could you email the name of the repository, your org and the VCS provider to support@deepsource.io or use our support page by selecting Report a bug option?