The actual amount paid to me by the management company is less than what is listed on the 1099 because of the expenses that were subtracted.
Perhaps I wasn't clear in my earlier post. If the 1099-MISC shows the amount of rent collected from the tenant, and it is more than what the management company actually paid to you, then you *CAN* claim/deduct those expenses paid by the management company, since those expenses were "in fact" paid on your behalf. This would include whatever amount the management company withheld for their own management fees.
I would also fully expect that you have paperwork from the management company showing you exactly what was paid by them on your behalf to other vendors. That's all the proof you would need in case of an IRS audit.
