I have cutechess-cli 1.1, platform is Linux x64 (Ubuntu). Not sure if this bug is still in current versions, but the issue is, options specified on the command line seem to be case-sensitive, while the UCI protocol spec specifies they should be case-insensitive.

For example:

-engine conf=$conf option.Threads=1 option.Hash=128 option."NNUE file"=arasan-d8-9-20210827.nnue

works, while

-engine conf=$conf option.Threads=1 option.Hash=128 option."NNUE File"=arasan-d8-9-20210827.nnue

fails with an error:

Warning: Arasan-23.0 doesn't have option NNUE File

The UCI option is declared on startup to be "NNUE file" (no capitalized f). I.e. Arasan outputs "option name NNUE file type string default".