I made strawberry jam, but after a few days there's this deposit. Is it something natural that happens, or is it a bad batch and I have to throw it away?
How much sugar did you add? The preservative here is sugar, and the mechanism of preservation is reducing the water activity so much that nothing else can grow. The resulting sugar jelly should be much denser than the fruit.
If you fruit sinks, the specific gravity of the jam might not be high enough.
I make jam several times a year and I never had this kind of deposit. I would throw the jam, I'm too young to die from food poisoning (like botulism, if there's not enough sugar).
Trust your nose and your tongue. Smell it, taste it; if it smells and tastes fine, then it's probably fine. (Strawberries are rather acidic and jam often includes lemon/lime juice, so the odds that it's something harmful are rather small.)
That said if I had to take a guess: you didn't skim off the foam while you were cooking the jam, and that foam jelled itself. If that's correct it's safe to eat.