I have got to debunk this thread.
1. I cannot find anywhere in that the IRS says "if you keep all or a part of a security deposit because the tenant caused damage that is considered rental income." This is accurate information, and if so please cite your reference.
2. Pub 957, 1099-MISC Instructions, and Topic 144 all fail to address these specific questions and most likely will be interpreted with bias depending on who is reading them. There are several different ways you could interpret the meaning incorrectly but let's step back and look at Box 1 "Rents" and Box 3 "Other Income". Did you collect rent or income that was not rent?
3. I even read a cross-post from Hijorst Fjoords referencing utility payment issues which are separate from this scenario. The CPA said it "...was an act of Tenancy..." and this also is not language that exists anywhere within the IRS publications.
4. Furthermore, The instructions on the back of 1099 tell the recipient to report the income in box 3 on Sch C. only if, "...it is trade or business income, report this amount on Schedule C or F (Form 1040)." Since it is not trade or business income, they report on Sch E and don't "kick out".
In Summary, was it a Rent payment? or was it not Rent (i.e. Other Income)?