There are a few automatic downvotes, which get attributed to the community user.
- Spam/offensive flags add a downvote
- Questions closed for certain reasons used to get an auto-downvote. They no longer do, but the old ones are probably counted in the totals you see.
- Very Low Quality flags that are dismissed as helpful trigger an automatic downvote.
Normally when a user is deleted, their votes are deleted as well. However, in exceptional cases, i.e. when removing all their votes would be disruptive to the community, their votes are transferred to the community user so they aren't deleted with the account. That most likely accounts for the upvotes.