I understand why option A is correct but I don't really understand why option E is incorrect.
Why are you saying that the underlined portion is an independent clause for option E and the same concept does not apply to option A

Here is the official explanation for this question:

Understand the Meaning of the Original Sentence

The sentence presents a fact about DARPA’s Falcon Hypersonic Technology Vehicle (FHTV). It states that this vehicle can fly as fast as 6 times the speed of sound. It can attack a target 2000 miles away in 30 minutes. Then the sentence presents the reason why such performance is achievable. The engine’s thrust is prevented from being dissipated in the stratosphere. This is because of the conical unibody design.

Find the Errors in the Original Sentence

• DARPA’s Falcon Hypersonic Technology Vehicle can fly as fast as 6X the speed of sound and can attack a target 2000 miles away in 30 minutes, its engine’s thrust prevented from dissipating in the stratosphere by its conical unibody design.

This sentence contains a single clause with the SV pair highlighted. The underlined portion of the sentence contains a modifier – a noun + noun modifier structure. This modifier provides further information about how the vehicle can fly this fast and can attack this fast and this far away. The sentence has no grammatical errors and communicates the meaning very clearly.

Review Answer Choices to do POE

Choice B – Even though grammatically correct, this choice distorts the meaning of the sentence since now it uses “verb-ing modifier” in place of “noun + noun modifier”. Thus instead of now presenting a mechanism of how the vehicle is this fast, it presents the following two meanings, both of which are illogical:
1.The vehicle itself prevents its thrust from dissipating – Illogical.
2.The vehicle goes this fast and this results in preventing its thrust from dissipating. – Reversed causal relationship - hence illogical.

Choice C – Same errors as in Choice B. Furthermore, “due to” is not used correctly. Here it may illogically imply that the dissipation of thrust is due to conical design.

Choice D – Use of verb-ed modifier in this sentence is not correct. Typically these modifiers are used to modify the nouns. Even if they are used to modify the clauses, they associate with the subject of the clause, and this is non-sensical in the context of this sentence as discussed in choice B analysis.

Choice E – This choice connects two independent clauses using comma. Semicolon should be used. Furthermore, this choice is very wordy.

TAKE AWAYS

1. Understand the meaning of the original sentence and determine the role of each modifier.
2. Be cautious of change of structure of modifiers since such changes even though grammatically correct may distort the meaning of the sentence.

Note: The attachment at http://gmatclub.com/forum/5-strategies-that-gmat-uses-to-distort-meaning-124296.html contains the document with Strategies for Meaning Change and the questions with detailed solutions. Note that this is a "living" document. We add the strategies, questions, and explanations in this document as we add them on the forum. So be sure to download the latest version!

EGMAT
Based on the discussion in the thread, I can see that option E is incorrect because
1. it had 2 independent clauses joined by a 'comma' and not by a 'semi colon'
2. 'being' is present in the sentence

But, I'm still not able to understand why are we
1. considering the two sentences in option E to be Independent clauses and the same is not applicable for the sentences in option A ?
2. Why is separating two independent clauses by a comma incorrect ?

Option A: DARPA’s Falcon Hypersonic Technology Vehicle can fly as fast as 6X the speed of sound and can attack a target 2000 miles away in 30 minutes, its engine’s thrust prevented from dissipating in the stratosphere by its conical unibody design.
Option E: DARPA’s Falcon Hypersonic Technology Vehicle can fly as fast as 6X the speed of sound and can attack a target 2000 miles away in 30 minutes, its engine’s thrust is prevented from being dissipated in the stratosphere because of its conical unibody design

Request you to help me with my query and with the concept of Independent clauses.

PS: I have already enrolled for the EGMAT's verbal course.

An Independent Clause must consist of a subject and a verb. Sometimes,there will be object or additional information for describing subject and verb.

Like, I am preparing for Gmat.
If you connect two IC, you can use the followings.
1. IC;IC
2. IC,(and/or/but/so/nor/yet/for)+IC

Ex. I want to pursue my MBA, and I need to get a good score on Gmat.

Let's check the first part of option A & Option E. There's an IC and we have no problem with it.
DARPA's Vehicle can fly.....,

Check the last part of option A.
..,its engine’s thrust prevented from dissipating in the stratosphere by its conical unibody design.
Here, prevented is not a verb, it's a verb-ed modifier. The construction is, its engine’s thrust is prevented .. by its unibody design. When we eliminate the auxiliary verb is, the sentence looks like 'its engine’s thrust prevented...by unibody design'
As there is no verb in the second part, we can't say it's an IC. Rather it's a modifier.
That's why, IC, modifier.

Now, check the option E.
DARPA's Vehicle can fly....., its engine’s thrust is prevented.. by its design.
In the first & second part, there's subject-verb match. clearly, there are two IC in this option. But they are connected by a comma. As we have already mentioned,two IC can not be connected by comma. It's a run on sentence.

I hope, the explanation may be helpful.

Thanks for you explanation, it was really helpful.
As mentioned two Independent clauses can be connected either by ';' or by ', FANBOYS'

Option E: DARPA’s Falcon Hypersonic Technology Vehicle can fly as fast as 6X the speed of sound and can attack a target 2000 miles away in 30 minutes, its engine’s thrust is prevented from being dissipated in the stratosphere because of its conical unibody design

Finally, is 'is' (helping verb) the verb for the subject 'engine’s thrust' in the second IC of option E ?
Second IC: its engine’s thrust is prevented from being dissipated in the stratosphere because of its conical unibody design