Some toppings are done while others on the same pizza are still raw or underdone

Affects quality

Almost always raw toppings with mismatched natural cook times combined without pre-cooking the slower ones.

Ask yourself

Which toppings were combined, and do they have very different natural cook times?
Were any of the slower-cooking toppings pre-cooked before assembly?
Were toppings cut to similar or very different sizes?

Likely causes

#1
Combining raw toppings with very different natural cook times in a single short bake
Strongly supported
A short pizza bake is not long enough to fully cook a dense raw vegetable or thick raw meat in the same time it takes to finish a naturally quicker-cooking topping.
#2
Slower-cooking toppings used raw instead of pre-cooked
Strongly supported
Some toppings (raw sausage, raw dense vegetables) genuinely need a head start before assembly; used raw, they finish long after everything else on the same pizza.
#3
Inconsistent cutting size for the same topping
Generally accepted
Thicker pieces of the same ingredient take measurably longer to cook through than thin ones cut from the same batch.

Rescue it now

If still assembling, remove and pre-cook the slower ingredient before returning it to the pizza; once baked, a brief broiler finish can help catch up any remaining raw spots

Prevent it next time

Pre-cook naturally slow-cooking toppings before assembly, and cut the same ingredient to a consistent size across the whole pizza

Italian sausage Cremini mushroom Bell pepper

Go deeper

Guides that treat this as an outcome to improve, an environment to work with, or a flavour to understand, rather than only a problem to fix.

How to balance toppings better Pizza in a wood-fired oven Pizza in a gas pizza oven How topping load changes the taste balance Mushrooms: raw vs pre-cooked on pizza Onion: raw, softened, or caramelised Why some pepperoni cups and chars and some lies flat Basil: before or after the bake Artichokes and other jarred vegetables: the water problem