I get this same error but not during bootup. My Pi can be running for 12+ hours and all of a sudden this error shows up. Very baffling to me, its almost like eth0 goes to sleep or something.
After you noticed this, please run
sudo dmesg
and check if there are any messages related to the interface eth0 (rather towards the end of the file).
Hint: The timestamps shown there are seconds since system startup.
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