Does this sound like a possible milk protien allergy?

My 12 week old has pretty much always been congested. She sounds stuffy all the time even after trying everything in the book to clear her out. It seems to be getting worse the past 4 weeks or so and is never really cleared out. She also has loose, explosive and increasingly smelly poop, sometimes there's mucus in poop. She seems gassy sometimes. Some days she seems happy, some she's extra fussy. She gets fussy on the bottle, pushes away several times before she will take it and fusses during bottles. Even when i know she's hungry.. (she gets upset before the bottle so I thought maybe it just takes her time to calm down) She spits up throughout the day. These symptoms seem to be getting worse as we give her more formula. With breastmilk she seems okay which we do feed breastmilk but I'm increasing her formula slowly. (I don't drink milk but I do have some cheese here and there.)

When I brought this stuff up to the doctor she said it's normal baby stuff and didn't seem concerned. But its getting worse so I sent another message and I'm waiting to hear back.

She's on a similac total comfort formula now.

Does it sound like it could be her formula? What formula worked for your baby with similar issues?