Basically when a large chest grabs glow that dropped on top of a crop it will also destroy the crop. I've noticed this happening only with glow but maybe other naturally generated loot might trigger this issue, like circuits or component kits dropped by bots, as long as they drop on top of a crop while a large chest is active and close enough to be able to grab that item.
I tried to manually drop items on the crops and let a large chest grab them and that didn't destroy the crops, so I'm assuming that it only happens when the items are dropped by other entities like glowbugs or bots.
Just to clarify I'm not talking about a vacuum pump attached to a large chest but simply a large chest by itself when turned on with a switch, also the crops that I've watched being destroyed were still growing.