I've seen this happen in multiple places– from Tetropolis to the flying beetle things in Frozen Flight– and more that I can't remember. Sometimes while standing on one of these moving platforms, Suit Link can't jump. So far I think I've only seen this happen in the deku scrub suit form. It's caused me so many deaths that I've had to start using the cheat menu to give me beat whistles at these parts.

Talking on behalf of the dev team, this issue has been already patched out by one of the developers.

This fix will be available on the next release :)