Well, I must say that the recent Gun Puppy change, while annoying, didn't make them THAT much harder but, saying that, even though this can be barely a change, it can be the most deadly scenario that could happen in an Arena match.
Like, for example:
The wave of 8 Gun puppies spawn and you still have 2 lumbers, or perhaps two Alpha Wolvers on your hands and only that tiny corner space to fight in, chances are you're going to alert the two Gun puppies closet to said corner, dodging that bullet fire while dealing with Alpha Wolvers or Lumbers in that tiny space is going to be very, very difficult, so your only options are to, run away from them to gain momentum back thus waking up the whole room, or tanking through damage and getting rid of them.
See what I mean by this change can be really deadly or absolutely no change at all?
While I am well aware that things don't always go as planned, the situation you described can be avoided with relative ease. Just make sure that you kill whatever is most dangerous to your play vs Gun Puppies and leave the other wave alive. Barring richots (damn you Alchemer line!) it should be easy enough to whittle each wave down to an individual, so you never have 2 to deal with. If you've counted your waves correctly, it should also be safe to kill that last mob, and then turn to the Puppies. Also, you can run to a different corner away from the mob while its busy with the death animation. The puppies only spawn after that's done, so you can get away without aggroing anything. This can buy you a lot of time with a Lumber or Jelly (not so much with an Alpha Wolver)