It makes perfect sense if your aliens are benthic marine creatures.
Falling upwards into the sky doesn't make sense if your aliens are humanoids living on solid ground beneath an Earth-like atmosphere. However, if your aliens are, instead, benthic life forms living at the bottom of an ocean, a disease causing them to fall upwards would make a lot more sense.
The disease would be caused by gas producing microbes. If they produced gasses at a faster rate than the organism could expel them, they'd become buoyant and float away. Creatures afflicted by "the floats" would need to wear weights whenever they wanted to go outside, in order to remain anchored to the seabed. Floating away would be fatal if the gasses were unable to escape from their host. As the afflicted creatures rose through the water column, the internal pockets of trapped gas would expand, rupturing their internal organs.
Inanimate objects could also succumb to the floats, provided they're suitable places for bacteria to colonize. Bricks would likely be immune, but objects made of wood or other organic materials could fill with internal gasses and float away.