On the left is the part with the negated part out, then the middle is it’s position, and the right it what it generated.
Model in Confidential section 
I’ve had this issue before. I tried again and got the correct Union when I moved the parts up .2 studs.
Not a fix but a work around.
I’ve also had this issue. I’m sure exactly what causes it, but it might be related to minute distances between sides.
If anyone at ROBLOX wants more examples, I can probably dig one or two up.