Found it!
Using a program Lossless Audio Checker I found that the files that do not play are malformed.
So it seems that MMA is working correct while MMW is doing a better job in laying files that should be marked as unplayable.

Would still be nice if MMA could do the same though.

I use MMW version 4.1.24.1883 and MMA 1.3.4.0854. Syncing was done over WiFi without conversion.
Most music is in flac format albeit there are som mp3 files as well. In total som 200GB ons my sd card on the (Android 9.0) telephone.
Some tracks don't play at all however. They play correct in MMW, but not in MMA. I can't find why. There is no additional codec pack for android as far as I can see.
Any ideas?

Thanks