@Robert-Moss I'm not sure if there is a file length limit. It could be that the file gets to big if processed and doesn't fit in the 32 bit RAM limit. You could split your file into multiple short files with some free tools like Audacity or you can use the free Samplitude Pro X4 from here http://dl04.magix.net/2019/SamplitudeProX4Silver/Program/SamProX4_Silver_INT_200121_07-59.exe It has many of the same tools as the Audio Cleaner app but a somewhat different interface. If the download link doesn't work just copy the link text(!) into your internet browser address bar and press Enter on your keyboard.
One question, are you using this app on macOS? If yes, then my advice to use Samplitude Pro X4 Silver will not work because it is a Windows application. But Audacity is also available for macOS.
Ah you seem to be correct. I was loading a download from Archive.org and although it was listed as MP3 it wouldn't load into Audacity either without loading a file called FFmpeg. Once it loaded into Audacity I could save it as MP3 and load it into Magix. This might be something that the authors of Magix might want to look into.
@Robert-Moss It sounds like the file used an audio codec that couldn't be decoded by Audio Cleaner but needed a different tool. Just if the file ending is MP3 doesn't mean it's an standard MP3 file. You can check the codec used by the original file in a free tool like Mediainfo.