The WAV file is correct, as WAVs can’t have a beatshift. I don’t see a shift there either.
The MP3 might not be getting seen by the beatshift scanner. I am seeing a shift there that is not being corrected. The beatshift generally catches 95%+ of the bad tracks so it might be that this track and some others are not getting recognized by the scanner.
The problem here is that wherever the MP3 came from, it was made with a bad encoder. So if you have other MP3s that come from the exact same place, chances are they have the same problem.
There is a way to prevent this from happening, by re-encoding your files with a more recent encoder and replacing the original file. You can use a tool like dbPoweramp or one of the many other tools that do it.
But you should do that before adding cues because re-encoding may shift them slightly (can be fixed manually in Lexicon with the Shift Cues/grid recipe). Give it a try with a few tracks before doing everything.
You have to completely delete a track from Lexicon (or a re-import from your Engine with merge disabled will also do). Then sync to Rekordbox and check the grid.
Check if the cues look good in Lexicon too, because of the possible shift from re-encoding
I think at the moment there is no fix for these specific MP3 files. They are not found by the beatshift scanner which is rare but sadly sometimes happens.
I don’t know where your files are from, but this will probably only occur from your files that come from the exact same place. You can try it with other files downloaded from a different source.
I’m not sure how Soundcloud works exactly but I don’t think they re-encode everything that is uploaded, so maybe these files are from a Soundcloud uploader that is using a program with a bad encoder. That’s all I can think of at the moment.