Trouble with whole milk?

My daughter just turned 11 months on the 3rd. Since then we have been giving her half whole milk and half formula in all of her bottles and she seemed fine with it. We got throw a half gallon and we are working on our second. Then two things happened, our son got the flu with a fever and vomitting then I fed her pizza with pepperoni. She has had pizza before but the pepperoni was a new addition I was letting her try. She puked her guts out as soon as she swallowed the pepperoni. She took a new bottle after a bath and puked all of that up to. Then she gagged thick spit all over me until she fell asleep on an empty stomach and she is still asleep. So any of the three things happened, shes not liking the whole milk (my fiances opinion), the spicy pepperoni was definitely not good for her stomach, or she got the flu from her brother. What do you think is happening and what should I do next?