I’m not an expert on how littlefs-python · PyPI creates the LittleFS exactly and what kind of debugging should be undertaken to find out what’s going on behind the curtain. As a general debugging step I’d recommend trying to unpack / list the contents of the generated spiffs.bin (actually LittelFS) with the tools given above, like mklittlefs. You should also try to mount and enumerate the LittleFS filesystem (there’s got to be some functions which tells you how big the mounted LittleFS partition is and a directory/file crawler enumerating all files).
For reproduction I’d also recommend upload your project (e.g. to github) so that other people can reproduce your project and problem 1:1.