As reported on our Discord support channel.
Test project by Discord member Half-Gray/7E7E7E
bass_test.mmp.zip

The arpeggiator sometimes triggers one arpnote to many at the end of a note with some settings.
Try turning up sustain a bit to trigger it.

The issue is there already in lmms-1.0.3 but not as obvious. In the test project you'll see a spike in the audio (mixer LEDs) when switching to a new held note. This goes away if you turn the Sustain and Release down to zero. The latest change happened in 67e9371 where the glitch becomes more prominent.

Edit: Superfluous bisect report moved to gist:
https://gist.github.com/zonkmachine/40e7000c2f93c68f0c55de2693ce27b0