It's very rare for a non grain grass hay like timothy, to cause any digestive upset, but also not unheard of for a rabbit in rare instances to be sensitive to a grass hay. Most common reason would be that the hay is a very soft leafy early cut and too rich, with not enough hard stems with indigestible fiber to balance out the rich leafy part. It's a bit like when animals graze on the first spring growth of fresh grass and get digestive problems. That new growth can just be very nutrient dense and too rich for them to be eating too much of it, so it can lead to digestive issues.
If the hay you have is very soft and leafy with little to no crunchy stems, then my guess would be that is the problem. Which would mean you would need to find a more mature cut of hay with more hard stems in it for the indigestible fiber they provide and that rabbits need for good gut motility. I like a grass hay that is a mix of leaf and stem. Not too leafy and not too hard and coarse with only hard stems. I've found that's the best growth for my rabbits to provide the needed nutrients from the leafy parts, and the fiber needed from the crunchy parts. You may still be able to feed the leafy hay, just not too much, and if you can balance it out with a more coarse grass hay.
If your hay does have plenty of crunchy stems, then it could be it was sprayed with something and that's causing the upset. I can't imagine any other reason unless your rabbit just happens to be sensitive to timothy hay. In which case maybe try orchard grass hay.