Why is a calorie not a calorie? Explain the difference between almonds and soda with respect to?

A calorie is not a calorie because our body is not a calorimeter- but a biological entity governed by hormones and other processes that a calorimeter doesn't measure or is influenced by. Hormones (mostly insulin) turn some calories into fat and other will get used by the body for other processes.

Soda calories are basically only simple sugars (carbohydrates) and almonds are mostly fat with some proteins and carbs.

When sugar is being digested, your body’s response is to produce insulin. Insulin is important to remove excess sugar from the blood, we can only have about 4g (less than one teaspoon) of sugar circulating in the blood at any one time. After eating/drinking a lot of sugar (carbs) insulin is released to remove the excess. It is then used by the muscles or brain, and everything that hasn't been used up gets stored as triglycerides (fat).
The more glycemic (insulin inducing) the food, the bigger the insulin response. Since soda is very nearly made entirely of very simple sugars and water, it is VERY glycemic.

The almonds macronutrient profile is roughly 50% fat, 25% protein and 25% carbs. Because of the fat, protein and some fiber, the body produces less insulin right away, and metabolizes these calories over a longer period of time, which means fewer calories will be turned immediately into fat, if at all.
You’ll also feel a lot less hungry.