This is not a poorly worded error message...
This has happened to me several times now and I am lvl8 with maxed out XM.
The first time it happened to me I had just used a Jarvis to flip the next closest portal that was fairly close. When the first one flipped it looked like both portals were flipping but they didn't. When I went to flip the second one it says... "Target portal already aligned." Which greatly upset me because it wasn't.
Today I tried to use a single Jarvis virus and I ran into the same problem and error message. I looked at the next closest portal and saw that someone else had used a Jarvis on it.
Both instances that this happened to me the next closest portal was recently flipped using a Jarvis.
I haven't tested this yet but... I'd like to see what happens if I attack the problematic portal with a single burster and then try to flip it so that the game understands that it is in fact still blue.