I've been fortunate so far to not have most of the problems others are reporting, but in terms of BGBuddy, I will agree that when there is more than one player using it, it's incredibly obvious. In watching it play, I can always tell when someone else is on BGBuddy. In AB, the current CTA, for example, the gates will open, the regular players will run out, and about 5 seconds later the bots will start. Their paths will 'randomize', preventing them from standing on top of each other, but they will go to the same base. If they're going to the mine, they stop at the top of the ramp heading down. If they're going to the lumber mill, they stop just outside the Farm/Stables. This pause lasts for about 15 seconds, then they continue. Thing is, you'll get two or three different toons all stopped in the same area. Again, 'randomly', so they're not stacked up, but seeing two or three people stopped at the end of the bridge from Stables to Lumber Mill (for Alliance) right after the BG starts, *every* time, looks suspicious.
As an aside, at least in AB, I haven't seen a whole lot of defending happening, just a whole lot of 'moving to biggest fight', and/or randomly running off to an enemy base by itself and getting pummeled. For example, I'm at gold mine wiping out a couple enemies. Fight ends, bot stops for a second to evaluate. There's some back and forth at the blacksmith, a couple people are trying to take the lumber mill, and a few people are on defense at the stables. It runs to the enemy-controlled farm, alone. I know, I know, logs or it didn't happen. Whatever. Run the bot a few times and look for these things, and you'll see it happening.