Software PWM (pins not directly hardware gate connected to timer hardware) has always glitches... You may not notice as long as the PWM 'frequencies' are low (on/off pulse widths are wide) compared to processor speed and to processor hogging code sequences.
I experienced similar issues with stepper motor(s) driven by Espruino, where timing is essential and irregularities can be heard easily: the sound/humming has a stuttering once in a while when running over a decent time at a constant frequency. With dimming this is not really an issue.
Electrical issues - instable rails - are a different story.
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