It sounds like you're talking about a Compliance Plan. The city of Oakland has been citing properties for a variety of reasons and before the property changes hands, you and the seller (I'm assuming it's bank-owned) need to agree to a Compliance Plan.
Your Realtor and the Listing Agent should be working with you on this situation (based on the citations it can be complex) and you will most likely have to pay a bond (which will be held by the city-not the title company) and make the improvements to bring the property to code. There are typically about $1300-$1500 in non-refundable fees (again, talk to your agent about who pays for these).
Compliance Plans with the city are involved and can be for so many different reasons (from expired permits to landscaping which has overgrown and become a fire hazard), so as far as your appraiser raising red flags it depends on the type of loan and what the violations entail.