There is only one pump on this machine so they all share one. The yellow and magenta share a cap top.
Cross contamination can be caused by a few things. The most common is failing maintenance parts such as cap tops and pump. If the cap top and/or pump tubes are partially clogged they will fail to drain properly which causes the head to dock while ink is still in the cap top which then gets sucked up into the head. Also, if the wiper is super dirty it will contaminate the head as well.
Dampers can also cause this. If one damper is failing and the other is working fine, it is common for the working one to become contaminated due to ink dropping out of the head while docked and it shouldn't.
If an ink cartridge is empty and not flagging the machine properly it will cause this issue as well.
And last but not least you have the dreaded punctured membrane. As with anything these parts do wear down over time. If you have new cap tops, dampers, the pump is working properly, you know fore sure your ink cartridges are not defective, and you still can't get rid of the magenta in the yellow, the internal membrane that separates the channels has punctured and will not be fixable. In that case you just have to spring for a new head.