This can happen when a process got it's capabilities through inheritance. Think of the following:
The parent process gives it's capabilities to a child proces, the parant process exits but the child remains running. If you start an LFS, change some ACL's and reload your config, LIDS will re-attach the capabilities based on the parents process capabilities and it's own capabilities. If the parent process is not running anymore the process will not get those capabilities again and may give errors.