Calories are the energy in food and if you don't burn it all it becomes stored as fat. However those calories can be made up of different fat/carb/protein levels, which some people keep an eye on.
For example I try not to eat anything too high in fat because I don't feel like my digestive system processes it well, I get very spotty with a high fat diet and it feels ironic eating high fat food when I don't want to be high in fat myself, lol! I also try not to indulge in foods which are too high in carbs because they tend to have more calories and I don't do enough exercise to justify a carb bing. I love high protein foods, because they make me feel fuller for longer.
So when it comes to milk I prefer semi skimmed because the fat and carb levels are balanced. whole milk has too much fat for my liking and skimmed has too many carbs. I only eat bread as a treat due to the carbs, same goes for cheese because of the fat. I think ham is good as long as it's lean and high in protein.
Obviously everyone's bodies process food slightly differently and have different tolerences to different foods, your lifestyle will also have an effect. So if you think a certain food is sabotaging your weight loss try cutting it out and see if it helps, if not perhaps your body is just trying to catch up with your loss so far, or your body had gotten used to functioning on less calories.
Unfortunately there is no one answer for everybody and what works for me is not necessarily going to work for anyone else.
Good luck xxx