Sentence Correction

Whereas the use of synthetic fertilizers has greatly expanded agricultural productivity in many parts of the world, an increase in their use can create serious environmental problems such as water pollution, and their substitution for more traditional fertilizers may accelerate soil structure deterioration and soil erosion.

A. an increase in their use can create serious environmental problems such as water pollution, and their substitution for more traditional fertilizers
B. an increase in their use can create serious environmental problems like water pollution, and if substituted for more traditional fertilizers, it
C. if these fertilizers are used increasingly, they can create serious environmental problems such as water pollution, and if used as substitutions for more traditional fertilizers, they
D. the increased usage of these fertilizers can create serious environmental problems such as water pollution, while if substituted for more traditional fertilizers, this substitution
E. the increased usage of these fertilizers can create serious environmental problems like water pollution, while their substitution for more traditional fertilizers

OA is A.
Now i know this question has been posted in the forums, but none of the explanaitons could justify the ambiguity in the use of the pronoun "their" in choice A.

Please help on this.