Both my elder yorkies went through this stage every now and then at different times in their lives!! I had to keep trying different things until I found a container they would tolerate. Jasper had a plastic bowl he liked, and Angel would not eat out of anything but a flat saucer. They are little nervous nellies, I swear. I think part of the problem was their dog tags and the sound it would make hitting the food container, but you probably don't have that problem. I am guessing your issue may be food related. If you found something your baby would eat with joy, it would not matter what you were feeding in, they would scarf it down, lol!
There are many food threads on here, I would recommend a search, and see what you would like to try. Just my humble opinion!
GOOD LUCK! At 3 months they cannot go long without eating!