I presume the OP is making an orange juice with "juicy bits", and IMEX <4mm sieving will indeed strip these out and clog up fairly quickly.
It's a tough one to balance without further FB controls of some sort.
I did note part 2(4)(d) of FSANZ standard 3.1.1 states that food is not suitable if it "contains a biological or chemical agent, or other matter or substance, that is foreign to the nature of the food". It therefore seems plausible that inherent physical defects associated with the orange cells, such as broken/embryonic seeds, would potentially be acceptable in some cases.
Beyond that I'd suggest the process for the cells themselves probably needs consideration, as for example I've seen fairly significant levels of metal filings/fragment contamination in them.
Whilst it's not within the scope of HACCP as such, there are also potential quality considerations in terms of physical "contaminants" even if they're intrinsic to the raw material, as whilst some acceptance of seed fragments is reasonable, excessive levels of these, or peel fragments that can darken and look unpleasant, are worth thinking about.
The best systems I've seen for cell processing use optical sorting before recombining with the juice, but this is (a) not cheap, and (b) potentially only viable if you're assembling the final product from a smooth orange juice component and a separate cells component.