Because natural gas is composed mostly of methane, a simple hydrocarbon, vehicles powered by natural gas emit less of certain pollutants than the burning of gasoline or diesel fuel.
(A) less of certain pollutants than the burning of gasoline or diesel fuel
(B) fewer of certain pollutants than burning gasoline or diesel fuel do
(C) less of certain pollutants than gasoline or diesel fuel
(D) fewer of certain pollutants than does burning gasoline or diesel fuel
(E) less of certain pollutants than those burning gasoline or diesel fuel

I know you use the word less when the noun is "uncountable" and the word fewer when the word is countable, i.e. you can put a number in front of it.

I feel like you can put a number in front of "certain pollutants", which is why I chose 'D'. For example, you can have 3 certain pollutants.

OA is E. Please explain. Thanks!

Because natural gas is composed mostly of methane, a simple hydrocarbon, vehicles powered by natural gas emit less of certain pollutants than the burning of gasoline or diesel fuel.
(A) less of certain pollutants than the burning of gasoline or diesel fuel
(B) fewer of certain pollutants than burning gasoline or diesel fuel do
(C) less of certain pollutants than gasoline or diesel fuel
(D) fewer of certain pollutants than does burning gasoline or diesel fuel
(E) less of certain pollutants than those burning gasoline or diesel fuel

B, D is incorrect. Pollution is not countable, thus less must be used.

A, C is incorrect. Those must be used to refere back to vehicles that's powered by gasoline or diesel.

I'm still getting stuck.

While I agree that pollution is uncountable, I still feel like pollutants are countable. For example, I know they count CO2 (a pollutant) - could be 385 parts per million.

* first of all, the point is moot, as (e) is the only answer choice whose parallelism is anywhere close to correct. the first part of the parallel structure refers to vehicles; (e) is the only choice in which the second part likewise refers to vehicles.

* fewer of those pollutants and less of those pollutants have different meanings.
the former means that, if you made lists of the pollutants from each of the two sources, then one of the lists would be missing pollutants that were on the other list.
the latter means that both lists would contain the same pollutants, but that the quantities would be lower on one side.

* finally, if a substance or quantity is measured with numbers and units - such as 385 ppm - you generally use "uncountable" constructions. for example, all of the following are correct (and the corresponding constructions with "fewer" are incorrect):
this cd cost less than $15.
i weigh less than 215 pounds / my body weight is less than 215 pounds.
the concentration of co2 in the atmosphere is less than 400ppm.
if you care about the underlying linguistic reason, it's because we aren't literally counting these units; they're merely a convenient representation of the underlying uncountable quantity, such as money, weight, or co2 concentration. if you need even more of a rationale, note that i could weigh 214.24235 pounds, and that the co2 concentration could be 375.239857 ppm; if these were countable things, both of those statements would be absurd.

How come E doesn't have a "do" at the end?
Without the "do", isn't the sentence ambiguous?
Without the "do", "those" can have two potential referents: "vehicles" and "pollutants".
Am I missing something?

if this is indeed an official problem, then you have just learned that the official answer to this question is "no, the sentence is not ambiguous".
take note.
remember, when you see an official answer with which you disagree (and there will be some of those), the idea is that you should learn from that answer, not fight against it.

--

incidentally, if the word "do" were to be placed into this sentence, it would NOT go at the end; that's not where those sorts of auxiliary verbs are placed in formal written english. rather, they come before the subject: than do those burning gasoline or diesel fuel.
compare this version with the version you'd get by placing "do" at the end, and you'll see the reason for the rule; the former is way easier to read and parse.