Current Arpeggio-engine in LMMS has some bugs. there are extra events, and some inconsistency. I would suggest that you use 'handmade arpeggios', and that can be done very easy like this
https://youtu.be/oQRJWTYtJ2c
This kind of arps can also do more creative music..
Later a completely new Arpeggio-engine, with new features will be introduced, but until that, you can do them like i do.