Not sure about the 1 out of 1000 calls, that would seem quite high in my opinion. I don't see that type of failure often, although I am referring to the XML-RPC calls. If there was too many of those, I would see far more errors or data issues.
Personally, I do not agree with the retrying of calls, because depending on what type of API Call you are doing, you could end up having duplicate data being added into Infusionsoft. An example would be like adding a new Order, but it oddly fails, then adding back the Order again. To be on the safe side, if it fails, you could do a check to see if it is added, and then retry again if its missing.
If you are getting too many failures, I would check the code, the server and connection you are using. If its the REST API failing too often, that is something Infusionsoft need to fix.