'issues' is a very wide term. 'indemnity' = to cover/promise something or to guarantee or to compensate (depending on how it's used) in the event of something happening. Without more information, I suspect that 'indemnity issues' = someone has promised to compensate someone else if something happens, that something has happened and now they are trying to weedle out of it.
Indemnify in the legal sense most commonly refers to one entity promising to pay the legal costs suffered by another party. If you sue a police officer for something he did during the course of his job, the government will usually pay any judgment that you get against him because they indemnify officers for certain acts done while on duty. In a lot of contracts you sign, you agree to indemnify the other side for any claims brought against them as a result of the contract.