It doesn't surprise me honestly since back in the day when Universal first opened there were major issues with Jaws and Kong for two examples. Due to the all the technology it had and the functions Kong had (for one example) the ride often had issues. One thing they did in order for it to begin to work more properly, they cut down the functions Kong could perform mechanically.
I think once Universal gets the hang of operating Gringotts, know how to upkeep the ride, and get a good balance of what functions it necessarily needs for the ride to make it a great experience without it being too much, it might not break down as often. I remember when FJ first came out, it often would have temporary break downs as well, and now it seems as if it's a well functioning ride now.
I'm sure it will be the same for Transformers as well, as I know Transformers has this issue as well sometimes (one time I went, the ride was not opened first thing in the morning, and even after over an hour it was still not being able to operate). Once again, because it's a new ride and the massive amount of new technology built into it I would imagine is one of the issues. But like FJ, once they get the hang of it (so to speak), I'm sure will will function just like any other ride.