Lately, I've been going to the gym and doing the stair machine and not using the watch (vivoactive) (because there are no native apps for those activities)...and instead I'm adding the activities in Garmin Connect Mobile after the activities are done. (The benefit of that versus using "walking" or the added activity app is that if you do it in GC Mobile, it'll populate calories whereas the other ones will give you worse calories estimates or none at all.)
Anyway, I went into active calories on the dashboard of GC Mobile and there are tons of calories from "walking" and tons from "exercise equipment". Seems like the software doesn't recognize overlapping data (in this case, the watch while walking up the stair machine, and the phone's added activity) and just adds them both.
Have you seen double counting in your data, too?