I guess the slow moving conveyer belt give animals time to get out of the way before getting captured. The Sea Cleaners FAQ also says the following.

Will this boat be a nuisance for the marine fauna and flora?

Every effort is made to minimize the impact on marine fauna and flora. In particular, the boat will be equipped with an infrasound system to keep marine animals away from the boat by scattering fish and marine mammals when approaching the boat.

Waste sorting will be done manually: the few living organisms and the organic waste that will get caught in the collection mats will be immediately put back into the water, without damage.

Except in special cases, anchoring will not be necessary, so the impact on the sea grass beds and marine flora will be minimized, and the calls will be scheduled in ports equipped with infrastructures to handle the cargoes of waste brought back by the vessel.

https://www.theseacleaners.org/faqs/