The problem with "I was wondering what are the differences between A and B" is that the segment "I was wondering" is a complete sentence and "What are the differences between A and B?" is a complete sentence. It sounds funny smushing them together without punctuation:
I was wondering: What are the differences between A and B?
I was wondering, what are the differences between A and B?
The problem disappears with "I was wondering what the differences between A and B are" because "What the differences between A and B are" is not a sentence and the whole sentence is more like the form "I was wondering what these are."
Restructuring a sentence because a bit in the middle is getting too long is okay to do but there are other ways to deal with the same problem:
I was wondering about A and B. What are the differences here?
There are several types of phrasal verb, and several types of verb + preposition. Not all of them are constituents, they serve different functions, they're all irregular as hell, and they're all governed by the matrix verb.
Every verb has its own assortment of special idioms, affordances, prohibitions, requirements, and irregularities. There is such immense variation in these details that such matters are considered part of the meaning of the verb; certainly they are strongly affected by the meanings. Square and cube that variation for phrasal verbs, since there are far more phrasal verbs in English than there are single-word verbs.
Some varieties can be examined in this freshman grammar homework problem. Examples of different types, from there:
Sentences (1) and (2) show two normal verb + prep constructions, from the same verb: look at, with transitivizing at; and look for, a transitive idiom meaning 'search'. Both of them require that the preposition precede the object (which may be thought of either as the object of the preposition, or as the direct object of the transitive verb + prep construction), even if that object is a pronoun. It makes no difference to most prepositions whether their object is a noun or a pronoun (ungrammatical sentences are marked with an asterisk *):
- I looked for Einstein ~ *I looked Einstein for ~ I looked for him ~ *I looked him for.
Sentence (3), on the other hand, is a real transitive phrasal verb. There are two characteristics of phrasal verbs that help to distinguish them. Both tests have limitations, however. The most important one, and the easiest test to administer, is the difference between the pattern of asterisks in the second and third columns, where pronoun objects force the difference.
There is a syntactic rule (called Particle Shift in the literature) that applies to transitive phrasal verbs only, and imposes a special requirement on pronoun objects. Thus, with a real phrasal verb like look up 'research (v)', the particle may appear either before or after a Noun object, but must appear after a Pronoun object.
- I looked up Einstein ~ I looked Einstein up ~ *I looked up him ~ I looked him up.
Note, however, that this test is helpful only with transitive phrasal verbs. There are plenty of intransitive phrasal verbs, too, but there's no object to test with. Many transitive phrasal verbs can appear also intransitively, e.g take off, move away, often with a different sense (He took it off ~ The plane took off), or not (He moved it away ~ It moved away).
The second useful characteristic is that a phrasal verb is stressed on the particle, at least as much as on the verb, and maybe more. A V + PP construction like look at, on the other hand, is stressed on the verb, not the preposition.
- He looked up the word. ~ He looked at the word.
That's because prepositions are rarely stressed, except for emphasis (In the toilet, you idiot!);
they're sposta slide by like articles and conjunctions to grease the way into the object, which is the informational part. They're not sposta distract, so they're unstressed, and therefore reduced, so we get common contractions like sposta and lookit.
Unfortunately, stress is not represented in English writing, so that distinction is not helpful for readers.
Best Answer
I found several entries for to get, in the phrasal verb section, so I thought I'd include them all. I separated them so the message is more comprehensible. Note that the last two are very similar except for the preposition "get sth over with" vs "get sth over to somebody". All the examples and definitions are mainly taken from the Oxford Advanced Learner's Dictionary, with a double check on my NOAD (for example, what I wrote between parentheses in "get over sth/sb".
get over something
To deal with or gain control of something.
get over something/somebody
To return to your usual state of health, happiness, etc. after an illness, a shock, the end of a relationship, etc. (Recover or overcome a difficulty)
get something over (with) (informal)
To complete something unpleasant but necessary.
get something <-> over (to somebody)
To make something clear to somebody.