There are many different answers to this question. First and most likely being that your Insulating Glass Unit or IGU has failed. Meaning the seal has lost its integrity and water vapor has come inside of the two panes. At first this condenses as a fog. It appears like the window is plain wet. Then in time the water will chemically etch the inside surface leaving a white haze. When it happens to an IGU with a low e film, colored spots might appear first. Or a type of colored haze. Which is usually pink but can take on other colors depending on the chemistry of the low e coating. When an IGU first loses its integrity the window will remain clear as thougyh there isn't a problem. There is a product which can be sprayed on the glass that will "freeze" the glass and cause any water vapor on the inside to condense on the glass. This will show up what otherwise cannot be detected. Most windows have at least a one year warranty. My suggestion is to check the warranty first to see if you can get a free replacement. At least of the IGU. The warranty usually does not include the work of removing the window. There are windows you can buy that can easily be removed. Both casements and double hungs. Then all you need do is bring them to a glass company for replacement of the IGU.
Second you might have staining from hard water spots. Most people cannot identify this as a stain. They think that something is wrong with the window. But not true. The spots usually come from the garden hose. Your local hardware store sells a product that you connect to your garden hose to clean your windows from the ground. No ladders needed! But the water left behind as water drops becomes hard water spots. Drops become spots. The spots are based on silicates and cannot be removed with windex or any other store bought cleaner. But will have to be professionally removed with a special product. Another phase of Glass Smart develops products to remove and protect against this type of stain. Especially if the spots have come from sprinklers. Unless you remove the sprinklers the spots will be back. Here is a picture of one of the compounds developed by Glass Smart. You can see how smooth and thick it is.
Third someone might have used a product based on a chemical that etches glass. This is usually hydrofluoric acid. But there are several other common chemicals too that will react with glass surfaces. The trained eye coupled with the right tests can easily determine whether your window(s) have been etched.
Fourth someone in the past might have sprayed insecticide on a nearby tree that got onto your window(s). Or someone might have used a siloxane concrete/brickwork hydrophobic sealant that ran down over the windows. Once cured it actually forms a covalent bond with itself and with the window glass. You will not be able to wipe it off with anything. The windows will have to be restored by means of a superabrasive compound and rotary polishing machines.
Fifth even pure water from a powerwash or rain can run down over a stucco surface and onto windows without a top drip edge, leaving deposits from the stucco. In less than thirty minutes such a stain will not come off with any store bought product.
Sixth but not last, windows can be very badly stained by steel/iron frames. These frames become rusty with age and leach out rusty deposits that lock into the pores of the glass. The more rough the glass the more prone it is to hold onto any type of stain. Such stains are usually black and white if they are on ordinary glass. But become quite colorful if they form on a low e coating on the weather surface of a window. Check out this.
This is an example of hard water spots caused by a sprinkler system.
