A bigger problem may occur when an addition was put up without permits and that addition happens to not meet specific zoning codes. The seller would usually file for a variance and that could take a long process. In this case the seller is the bank. Are they going to lend you money for a home that is lacking a c of o?
You really need to specify why it's missing a c of o because are you going to take on that responsibility of having it fixed? REO properties are generally sold "as is" meaning that the bank will not be responsible for getting anything done and that is reflected in the price. Your agent can attempt to negotiate on your behalf but honestly you'll probably need to assume the risk.
I'd call the town inspector to see if he can shed some light on the reason for the missing c of o.