It depends on the rattle, of course.
If it's noisier injector clatter, it could be a change in fuelling - expected when the filter is changed and the relearn isn't triggered (easy: reset the ECU). Have you changed fuel brands? Did you refuel from a small servo (possible low turnover = old fuel, or water-in-diesel)?
If you suspect it's coming from the housing right at the front of the motor (tip: buy a $25 mechanic's stethoscope from SCA) then it could be your timing chains. While there haven't been a huge number of failures, the YD25 timing chains aren't the strongest. If they break, we're talking valves-into-pistons, cracked valve guides, scarred cylinder bores, maybe even damaged camshaft bearings and it could cost a small fortune to repair. If it IS your timing chain, don't replace it with a genuine part - talk to Paul from yd25.com.au and order the upgraded chain. Takes a bit to install it, but you'd never have to worry about it again.