I get this but the project was made with KiCAD 9.0.1 and all components are correct.
Of course I can ignore it but I would like to understand what’s causing this.
NOTE: version info after the screenshot
Application: KiCad PCB Editor x64 on x64
Version: 9.0.1, release build
Libraries:
wxWidgets 3.2.6
FreeType 2.13.3
HarfBuzz 10.2.0
FontConfig 2.15.0
libcurl/8.11.1-DEV Schannel zlib/1.3.1
Platform: Windows 11 (build 26100), 64-bit edition, 64 bit, Little endian, wxMSW
OpenGL: NVIDIA Corporation, NVIDIA GeForce RTX 4060 Ti/PCIe/SSE2, 4.6.0 NVIDIA 566.36
Build Info:
Date: Mar 30 2025 01:11:30
wxWidgets: 3.2.6 (wchar_t,wx containers)
Boost: 1.86.0
OCC: 7.8.1
Curl: 8.11.1-DEV
ngspice: 44
Compiler: Visual C++ 1942 without C++ ABI
KICAD_IPC_API=ON
Locale:
Lang: en_US
Enc: UTF-8
Num: 1,234.5
Encoded кΩ丈: D0BACEA9E4B888 (sys), D0BACEA9E4B888 (utf8)
Have you tried selecting the component in question and then, under Inspect . . .

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Yes nadit returned me this:
but I have selected that footprint on the schematics from the KiCAD library. Anything fancy or strange.
And KiCAD seems do not recognize it (?)
Generally, this means you modified the footprints in your project in some way, and they no longer match the footprints in the libraries.
KiCad’s standard libraries are read-only. If the modifications were intentional and for this project only, then you should mark them as exceptions in the DRC. If you intended to save the modifications for use in other projects, you should save the modified footprint to a user library and reference that in your projects.
I get the same warnings since i updated from KiCad8 to KiCad9 with symbols and footprints that i selected and are autogenerated footprints. I did not change anything. The solution for the problem was to place all components again and for 4 headers just excluded them. Also some components i had i did get this as error but that was correct since i renamed my (user) library .
I never modified these footprints.
And the footprint CE_logo I added it directly in PCB without any modification.
R1 and R2 are selected directly form KiCAD library without any change.
Me neither. I got the warnings over scripted autogenerated footprints in the kicad directory in program files. I solved it by selecting the components again and manually added the refdes. Other auto generated components i just excluded from the inspection. If you exclude a component , the warning is still visible but the warning is not counted as a problem. This all happened when i switched from kicad 8 to kicad 9. Perhaps some readonly libraries got a new name under kicad 9, or the path is not correct ?
I have experienced this and it is usually related to something I did. However, there have been instances where I get that error message and the cause is a mystery.
In the PCB Editor I usually select “Tools->Update Footprints from Library…” and that resolves it, usually. When that move creates more issues I use “Ctrl-Z” to back out.
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Thank you for the suggestion. This helped.
The “CE” marquee was replaced by a huge one.
I had to delete it and reselect the smallest one.
Why did it? Not clue. However now I have not any warning
I selected the components manually, Pressed E and i selected : “Update footprint from library”
I tried this and this resolved the warning issues for me as well. I guess this is a necessary item to do when migrating from kicad 8 to kicad 9. That is solved. 
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