The mods that were MJ based were always somewhat prone to exploding should things go wrong. So, chaos would start like this:
A player would log off / leave the area of their base.
Implicit chunkloading (and some residual power) would keep a quarry alive. Which would pump items into pipes, which would travel through BC pipes in the laoded chunk until they hit a boundary...
Buildcraft pipes could explode if overloaded, so this would then force load the next chunk - allowing items in pipes in that chunk to keep on flowing into neighbouring chunks, force loading them.
So a quarry being chunk loaded then implicitly forces the chunkloading of a bunch of other chunks.
If any of these chunks happens to contain your power generation, then the madness never stops as the quarry is being fed fresh enenergy to keep on going.
So, your immediate problem is water. It is very easy to put a pump - or liquid pipes carrying water - in non chunkloaded chunks. And liquid pipes - unlike item pipes - don't chunkload. This means if your power source is combusion engines or railcraft boilers, its very easy for the patchwork chunkloading taking place to starve them of water.
If you are cheesy and just build an infinite water source in the same chunk as your engines/boiler then at least things won't blow the @#$% up.
The perdition mechanic that buildcraft had however added even more evil: all the devices in chunkloaded chunks would consume energy, the power plant would consequently never shut down, and liquid fuel reserves (BC oil based fuel is non renewable) would be exhausted doing nothing while players on servers were offline. I presume the modern quarry works on RF with RF mechanics - no energy consumption when its not running so now your only real problem is the potential to overload your sorting / storage system while you are offline and unable to deal with it.
If your fuel source was renewable, but required energy, you still run the risk of running out of fuel if the implicit chunkloading doesn't cover the farms, so starting everything up if you log on and have zero stored energy and fuel could prove problematic.