I ran the following commands for various libraries to move the libraries to a sub-site. In doing so libraries inheriting permissions continued to inherit after the import/export. Libraries with unique permissions only had the secondary admin account I used in the ACL of the problem libraries. No errors were observed in the import/export logs. Why would this have occurred?
Export-SPWeb -Identity "https://sp.domain.com/sitecollection/site" -ItemUrl "Library" -Path "\\Server\Library.cmp" -NoFileCompression
-Force -Verbose -IncludeVersions All -IncludeUserSecurity
Import-SPWeb -Identity "https://sp.domain.com/sitecollection/site/subsite" -Path "\\Server\Library.cmp" -NoFileCompression -Force -Verbose
-IncludeUserSecurity -UpdateVersions Append