Unless military tactics dictate that they try to "hide" in the cone since they first picked up our radio signals... Even If they're on a "civilian" mission, they might have navigators/a captain with military training...
a) Tabby's Star is roughly 1500 light years away from us; we only began emitting radio signals ~150 years ago (at most -- assuming propagation from early telegraph wires; not actually very likely) and it'd take ~3000 years for our signals to reach the vicinity of Tabby's Star and indications of a reaction getting back to us,
b) "Military" is a category error on this scale; the energy budget required to generate the sort of luminosity changes we're seeing around Tabby's Star by deliberately occulting it are mind-blowing compared to anything we've ever achieved. Might as well speculate about an ant-hill (us) wondering about the military intentions of an M1 Abrams tank driving across the Iraqi desert (hypothetical alien actors at Tabby's star) -- either they aren't going to drive over us, or we just encountered an Outside Context Problem.
