Since our opening modifying phrase mentions problems in mathematics, we need to start the underlined portion with something that logically fits.

A (engineering and technology) does not, so it can be eliminated.

B, C, D, and E all start with a phrase modifying our initial phrase, so we need to look a little bit further in to find parallel form.

B. almost always having a unique answer, many different solutions can be found for a single problem in engineering and technology
C. which almost always has a unique answer, there are many different solutions for a single problem in engineering and technology
D. which almost always have a unique answer, a single problem in engineering and technology can have many different solutions
E. rather than almost always having a unique answer, a single problem in engineering and technology can have many different solutions

E uses "rather than", which we don't need because we've already used "unlike" to indicate a difference. D is the best option.