This is an unfortunate problem to be having, especially since you know that you have a need for vitamin D. In general, most people will respond very well to supplementation with something as common as vitamin D. In your specific case, it is possible, and even likely, that the heartburn and reflux started about the same time for some other reason (such as eating right before bed, increased stress, or more caffeine), rather than because of the vitamin D. That being said, it would be appropriate to skip a few doses, or change to a different brand, and do a test to see if your symptoms improve. You should not, however, just completely stop taking your vitamin D for more than a few days, as there are many long term side effects (such as decreased bone density that can lead to fractures, among others) that can come if you were to have low vitamin d levels for a long period of time.
If, after trying to either change brands or stop your vitamin D for a few days, the symptoms go away, then you should tell your doctor
and switch to a new kind that works for you. Alternatively, if the symptoms persist, then it is likely not due to the vitamin D at all. Talk to your doctor about new heartburn, as there are excellent treatments available.