Handling duplicate entries with the same parent ID

When the same hook is called twice within the same function, the check for an existing ID will come up as true, even though the meta (e.g. line-number) will likely be different for the second call as the first call. Equally, if functions with the same name are defined twice, perhaps in the global namespace (parent ID = 0) in different files that are not included within the same request, they too will have different meta data and should be different entries.

Perhaps a join to postmeta table on the existing ID check and also compare the file and / or line number would narrow it down?

If the same hook is being called twice on the same line in the same file, well, that's just stupid! (But technically plausible.)

Start by tracing the existing ID check for repeated hook calls and inspect how entries are matched against the postmeta table. Verify the behavior for repeated calls with different file or line metadata, and for same-named functions in separate files. Done means distinct metadata produces distinct entries while identical calls remain handled consistently.