IP3000 cross contamination - cause?

[Ink stained Fingers]

This sounds like an argument for refilling all your carts as soon as the printer sounds the "ink is getting low" alarm on any one of them.

Yes, and there is another good reason - every cartridge change triggers a purge action, and if you fill up all cartridges at the same time you can save lot of those cleaning cycles, saving ink and prolonging the the life of the waste ink container.
The situation is tricky - there are minute pressure differences between the cartridges which are connected to each other when resting on the purge unit, I have seen black contamination in yellow carts, and a few times as well in the magenta carts after some days. But beyond that don't let inks drop and prevent any mess this way. Getting the foam soaked is pretty easy - fill up the chamber , close the refill hole and place the cartridge on the side for a while, the ink will migrate into the foam, and the ink level in the chamber will drop somewhat which you can top off again, but this would depend on your refill method.