I’m not sure if I understand you correctly… What do you mean by “I put the program into the Windows folder”? Are you talking about C:\Windows here? Please remove it there, thats the OS’ space and shouldn’t be touched by you.
From what you describe otherwise, it seems to be a discrepancy in PATH between both environments. Usually bash will inherit the PATH of the parent environment (windows system in your case), at least if you are using a bash from a POSIX compatibility layer as cygwin or “git for windows”. You might have overwritten it in the .bashrc then though.
If though you use the WSL-bash then it has its own environment and does not inherit from windows at all, as it is a “real” linux and wouldn’t be able to run windows binaries anyway.