Controllers, solenoids and other pheripheries are connected together with low voltage wires. Because there might be lots of connectable electrical components in the same location but far from the centre unit, multicore signal cables are commonly used in an irrigation system.
Different color wires go to different components and this is the easy way to differentiate on both end of the cables.
As long as the low voltage cables don’t need special protection, sometimes they are laid down near the ground surface or even on it. Hence there is a good chance to get damaged.
Most important thing is to make sure it cannot happen. During groundworks, make sure they are marked when they are found.
If a multicore cable has been damaged, it’s not the end of the world. Call an irrigation engineer and let him/her reconnect the wires on the right way. If you do it on your own, make sure, identical colors are connected together.