The CAR contract is more generic and requires the users to fill in more check boxes for who will pay for who, who is responsible for what, etc.... Miss one box and there are lots of questions and potential problems. Most agents who work in SF, don't know the form well, so there is more opportunity for mistakes.
Hope that answers your question.
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Over the years both contract forms have been updated and improved and continue to be updated on a regular basis. My personal opinion is that the San Francisco contract is less convoluted and easier to comprehend than the CAR contract. It's shorter (7 vs. 8 pages) and, as an example, you don't have to look in two different sections to understand your inspection contingency.
It's also true that there is language in the San Francisco contract (that's not in the CAR contract) dealing with San Francisco-specific issues such as TIC and multi-unit property purchases.
Some contracts will include conditions which need to addressed before closing, some will make agents a party to the contract, etc. The CAR contract was written my a larger member audience, it is an AS-IS contract, agents are not a party to the contract (which they are not a party to the contract), etc.
The biggest difference is not all agents are familiar with local contracts, but all agents should be familiar with CAR as it was the only acceptable contract for the last few years in Short Sales and Bank Owned Properties.