Thanks for getting in touch, this is a strange one. We've seen it at least once before but have not been able to reproduce it. Our suspicion is multiple threads causing the issue, in version 3.11.18 of Octopus we put in some safe guards to make IIS deployments more reliable. If you can you can try and update to a version after that to see if it solves the problem: https://octopus.com/downloads
Could we get some more details from you to help us work out what's going on. What version of IIS and on which version of Windows is it running on, and which version of Octopus are you currently running.