Was your CPA well-prepared, with copies of all receipts and payments, as well as a detailed understanding of your company? Without seeing the case set out in gruesome detail, it's impossible to say what happened. Is the company successful for three of the five years to prove it was a business and not a hobby? It is your responsibility to prove the deductions; it is not the IRS's responsibility to justify why they should not be permitted.

The less structured the presentation, the less receipts, documents, and so on, the more likely the deductions would be disallowed. Expenses must, of course, follow fair and appropriate requirements, and employee business expenses are even more stringent due to the likelihood of reimbursement from your employer. 

They can't be just personal expenses, either (makeup, general clothes, haircuts).

What was the essence of the out-of-pocket costs? Certain products, such as those described properly, are prohibited unless extensive usage records and specialized documentation are provided.

How many audits had the CPA already completed? How many hours did it take to prepare? Has your representative specialized in audit protection and serving taxpayers at examination by courses and continuing education?