They should not be clumped together because the two conveyors and funnels in the current machine design will place the beans into a single line, with enough distance between them so that each can be removed individually.
Throwing out the whole group of beans together would also be an option, though. Commercial optical sorters do it similarly: they create “first rejects” in a first pass, which includes some good beans. The first rejects are then fed to the machine again. This time, the beans will be grouped differently and so the machine will only throw out the bad ones (with a few exceptions of course). These are then called the “final rejects”.