The mentioned plugin(s) needs to be cleaned. Pay attention to similar LOOT messages.
A deleted reference is a record in a game plugin that has the "Deleted" flag set.
Deleted references can cause CTD if they are referenced by other records or otherwise used indirectly.
See xEdit Cleaning and Error Checking. Clean every plugin that LOOT suggests to clean - ignore misinformation that cleaning any plugins is not needed, does not do anything or causes problems. While ITMs are irrelevant in this context, see There are no intentional ITMs. The Batch Plugin Cleaner for Mod Organizer or the xEdit Cleaning Extension for Vortex help to automate some of that. Ignore misinformation that cleaning any plugins is not needed or causes problems.
If a master record is deleted (or permanently disabled via the enable parent opposite to player) and it is not referenced by any other record, it can most likely be removed from the plugin entirely.
Deleted references are ignored for LOD.