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If you are in breach of lease in that it states only 2 people can occupy the premises, then the landlord has a right to hold you in breach and seek to negotiate a new lease with you or can seek to evict you if you do not cure the breach. Legally, you can claim that his knowledge and failure to take action when he knew about the breach was a waiver of the breach under the laws of equitable estoppel and waiver.
A child does count as an occupant in CA, though, so legally he could claim you are over the two occupants clause. You would have to fight him on this matter based on the fact he knew that your father was there for 9 months and took no action. Thus, this would not be something that is an illegal action that could be reported to the local housing agency, it would be something that you would have grounds to fight him over if he tries to evict you before the end of your lease term based on his knowledge that your father was there and failure to take action in a timely manner under the equitable theory of laches and waiver, and as such you would argue he should be estopped from raising the rent until the new contract
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