You know, 3 months is still pretty young. I don't know if this is appropriate, or when it would be, but... I think there comes a time when you have to let them know that the behavior is not acceptable. For a while, Lexi had run of the kitchen. But we were having major construction done, and there were times when work was being done in the kitchen, or the workers were in and out, and we'd have to put her in her ex-pen. She didn't like that, and would bark - especially her high-pitched "I don't like this" bark. Very hard to take...
When she would start to bark, I would go over and in a firm low voice, say, "Quiet." You need to be calm and assertive. At first, I would also lift one section of the ex-pen just a bit and push it down on the floor. The noise was a bit startling - not super loud, but like a surprise - and not exactly something anyone would enjoy and ask for again. It didn't take long before we could say quiet without banging the ex-pen. And after that, sometimes words weren't even necessary. Just walking over and giving "the look" was enough.
Nothing horrible was done - she wasn't yelled at, hit, or punished. We just let her know, firmly and calmly, that the barking was not okay. And it didn't take too long before it worked.
And yes... I did feel badly, and wished she didn't have to be in there! But sometimes, that's life, and we just have to deal with different things on different days.