I mean the whole "matrix glitch" thing is a fun idea, but it's way more likely to be a simple edit mistake. When you're cutting between shots, especially in nature footage, it's super easy to have a jump cut where something looks like it vanished. Or maybe it was just the wind moving branches so the shape changed. Idk, maybe it's just me but I've done video work and this happens all the time with shadows and angles. Our brains are wired to see patterns, so we jump to a cool story, but the boring answer is usually the right one.
Oh man, I'd probably blame my own editing skills before I blamed the simulation! I once spent an hour looking for a clip I swore I saved, only to find I'd just renamed it something dumb like "tree_final_final_really.avi". Our brains and software are both pretty glitchy.