Dan:
There are no chemicals in the BondTite which will cause bubbles to be formed - usually bubbles in the primer coat are a result of air in the concrete. If the slab or ambient temperatures rise while the BondTite is still wet, air entrapped in the concrete will expand, when it does that it has to go somewhere, BondTite is that somewhere.
The size of those bubbles can vary from almost invisible, to saucer sized, it depends on the temperature rise, and more critically the composition of the concrete, some just have more air entrapped.
If the bubbles are small, say small enough that you can't feel them when you run your hand across the BondTite, no prob, just over coat with LiquaTile. If they're larger, and form a small dome, then there's the possibility that their profile will "print" through the LiquaTile, or if they're really large they could even poke up through the LiquaTile. Neither case is good, so they need to be taken care of before the LiquaTile is applied.
That's done by simply sanding them down. If there's not too many of them, just use a block sander or a palm sander. Even if there are a lot of them a small sander works, but it sure can be rough on your back. So if you have a huge area, and a lot of bubbles, consider using a floor buffer with appropriate media. The BondTite will still be relatively soft, so the media doesn't need to be too aggressive. Even the ones that are essentially large ScotchBrite like scrub pads will do the trick.
Now then, if a bubble is too large it's possible that when it's dome is sanded off you'll notice that at the base of the bubble there may be a void, that is there will be a small spot where there is no BondTite, but just bare concrete. Usually this isn't an issue, the LiquaTile is self priming, and although the concrete/epoxy bond will not be as good as with BondTite, considering it's such a tiny spot, and it's surrounded by BondTite primed areas, the LiquaTile will work fine.
Whatever the bubble size, after you sand them down and before applying the LiquaTile, quickly wipe up any residue, although there won't be much.
BTW, the best way to avoid the bubbles forming in the first place is to apply the BondTite as the slab and ambient temperatures are cooling, so try prime in the late afternoon or evening. Even with decreasing temps you may occasionally see bubbles, although it's far less likely.
Another possible source of bubbles is over agitation or drawing air into the epoxy while mixing, avoidable by keeping the mixing paddles fully submersed and/or using a lower speed.