Coffee and especially its key ingredient caffeine have been shown to lead to weight gain in several studies. One from the Western Australian Institute for Medical Research wasn't even looking into weight changes but came upon it in their data. They found that too much coffee, including decaffeinated, resulted in a change in the utilization of fat in the liver and caused abnormal retention of fat within cells. This resulted in a higher degree of glucose intolerance and increased insulin resistance. Caffeine in particular has been known to stimulate cortisol production. Cortisol is the stress hormone that was originally designed to give us a jolt to face a danger or stressful situation. This helped to save us from an imminent physical threat. Cortisol serves another purpose in that it promotes the release of insulin which we need to move glucose into our cells.
When you have a stressful period you typically feel an increased hunger, because cortisol is creating a run on blood sugar.
What's most surprising is that caffeine is included as an ingredient in many weight loss aids. While it may temporarily result in some benefit as it stimulants the nervous system and may increase metabolism, that effect is temporary and negated by the increase in cortisol and increased fat retention. For those that consume coffee after 2pm it may lead to decreased sleep, less sleep can lead to increased cortisol levels which would result in more eating.
Caffeine can induce hypoglycemia. It's thought this is because it impairs glucose metabolism. Glucose is a very critical source of energy for cells the body constantly works to keep the fuel flowing and within a normal range so you feel good and can continue on. When hypoglycemia comes on it results in headaches, fatigue, mood changes and a beating heart. Caffeine inhibits the release of GABA, which keeps us alert and is used by our body to communicate between nerve cells. When GABA is low it can result in anxiety and mood disorders.
On its own a cup of coffee only has a handful of calories but many prefer to add, cream, sugar and milk - this can easily add 100 calories. In fact, a latte can easily have as many calories as a piece of pizza as it's loaded with milk and sugar. Because of all these reasons many people have found that after quitting a long regular use of caffeine they experience weight loss.