Water in Oil?
 

Changed the oil in my 2005 Expedition and noticed a bunch of light brown gunk around the filler tube for the oil and in the inside cap. Is this from water getting into the oil?

More likely just condensation, unless you found the oil you took out to be that way also. A lot of people here have reported the gunk situation, and more often than not it just that.

Oil was black. The oil filter seemed like it something in it also. It was heavier than normal and you could feel something moving in it when you shook it.

I had the same problem but mine just happened out of nowhere, turned out my head gasket had a small leak in it, fixed that and it stopped. But I had a lot of the sludge in my oil fill neck. Most likely you have condensation in your oil from short trips. It is normal for it to build up, just use good oil and you should be fine.