Are you sure that the file there is .htaccess and not htaccess.txt? Code integrity check problems with .htaccess are probably the most frequently asked question here, and it almost always comes back to the same solution. Make sure that after the files are unzipped from the Nextcloud download, and they’re copied to wherever you need them, that hidden files are being copied also. The standard copy command usually doesn’t move hidden files if you use a wilcard (eg cp /nextcloud/* /wherever/ ) but will if you just copy the whole directory (eg cp ./nextcloud /wherever/ )
If you really do have the .htaccess file showing in your root directory (as opposed to htaccess.txt or htaccess-sample.txt or whatever the sample .txt file is called) and code check isn’t seeing it, then I’m less sure about the path forward. Let us know.