data/stable_api.dat is a bespoke data file consumed by the custom limited-api-list directive to produce the limited API list, and IIRC to also automatically annotate APIs that are part of the stable ABI.
Presumably the custom limited-api-list directive does not set node.source on the affected doctree node (while node.line is set), either unintentionally or because technically speaking, there is no one specific source file for the content, it is generated by the directive.
This does come from an extension: specifically, the limited API list generated from – you guessed it – stable_abi.dat.
I commented on the issue that added PyExc_IncompleteInputError: #113744
The others look pre-existing. They should be added to Exception Handling — Python 3.12.1 documentation – usually as a link to the Python exception, which in turn needs docs as well (unless the C name is a backwards-conmatibility alias to a documented exception).
Ideally, the extensions would emit something useful instead of <unknown>. This particular extension is at c_annotations.py:199; other extensions might want similar fixes.