Hi Barley
You could have a couple of things going on here.
First of all, your baby is 12 weeks you say, and this is one of the ages at which babies have a major development point, during which it's common to lose their appetite a bit. Does he have any of the other signs, such as excessive crying, increased demands for attention, wanting to feed more often even though he doesn't really eat (sucking can be calming in babies of that age), wanting to be close to mum, seeming to be shy with others, sleep disturbances such as not napping well, taking ages to get to sleep, waking through the night for first time in ages? If so, then his appetite will return as everything else calms down.
The other possibility, which I think is much more likely from what you've said, is what is known as lactose overload. You say he cries during the feed. Does he writhe or wriggle a lot, seem to be in pain, curl up, pull off the bottle and scream then want back on quickly? Oh, how about his poo - has it changed lately and what colour is it? Is it stickier or smellier than normal, or perhaps frothy or explosive? Does he seem to have bloating, cramps or excessive gas?
Lactose overload can occur in a bottle fed baby when the milk flow through the teat is too fast. The baby's digestive system can't cope with the volume of milk, which passes through the digestive tract too quickly for the lactose to be digested. Feeding makes the baby's intestines contract, pushing the food through. If fed too soon after the last feed, this can mean some milk gets pushed through into the bowel, where the undigested lactose then pulls in extra water and is fermented by the natural bacteria in the bowel, producing gas. The gas is what can cause the cramping, bloating, pain, wind and acidic green poos, that can hurt your baby's bum.
Because the action of feeding provides the baby with temporary relief, they will want to feed more often and so you think they're hungry and feed them again, causing the problem to get worse.
The first thing to do is stick to regular feeding times, even if you think your baby is hungry sooner. Then, when you do feed, keep the baby as upright as possible and the bottle horizontal, so the teat only half fills with milk. Your son will be able to take only what he needs.
You should notice that the crying stops after a few feeds and that any other symptoms are relieved within a couple of days.
Good luck