In my experience the Pyramid is very stable. Bugs are of course always a possibility - in all involved devices! See eg https://forum.arturia.com/index.php?topic=90169.0
Anyway, I’d start by verifying sync settings on both ends.
Is the missed beat truly random or actually something like every n’th one?
Truly random suggests clock or hardware issues of some sort, periodic issues are more likely something else: Different signatures and track lengths together with polymeter/polyrhytms can create all sorts of “interesting” effects in relatch mode too. Then the live looper feature can apparently affect the start step: Track start step wrong. Another sort of related common issue is missing the first note of a sequence because it’s timing is a little early, but then it plays when looped.