I noticed this when I was hitting an enemy command center in a planet adjacent to one of my planets with transports - they instantly lost 1/3 of their health. After I stopped freaking out, I checked the planet (Coundic) in the galaxy map, and it says that it isn't in supply even though I own an adjacent planet (Juasiur) that has a completed command center. Even more oddly, another enemy planet adjacent to Juasiur (Tolyepih) IS in supply, and I confirmed this by sending transports through that wormhole. They lost no health.
Save is attached. Cluster in question includes my easternmost planet, which has a ton of ships on it so it should be obvious.
EDIT: Version used was 3.114, still exists in 3.115 as well, not that I expected that to fix it.