Im in a three person llc partnership(S-Corp) and one of my partners wants us to pay for an apartment for her and her family. I question this because 1.) she isn't the best housekeeper, I can for see us not getting our deposit back if she eventually got her own place. 2.) she wants parts of her salary to not be reported/taxed. I don't want to get to a place of comingling funds. Also, a majority of her salary comes from sales. If her commissions do not cover all her apartment costs one month can we legally not pay her, her standard/regular (non commission based) salary to recoup the costs? We are in California.

What is the nature of the business. But I would tell her no. That she should keep her personal expenses apart from the business.

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Im in a three person llc partnership(S-Corp)

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No, It is one of those, not all three. It is either a partnership, a LLC (limited liability company) or a corporation which has elected to be treated as a partnership for tax purposes (a "Subchapter S corporation"). That is like saying you are married but single: an oxymoron.

No, it would be improper for your company to lease a residential apartment for the use of one of the owners of the company.

Do not fail to report part of her salary unless you want to get into serious tax problems. In addition, you need to see an accountant to see that you are not in tax problems already. By what you have written, I would be surprised if you are not.