Some words, such as 'number', have so many different meanings and uses that it's difficult to know and understand them all. However, I find it a good starting point to trawl through all the definitions, and see if you can find one that fits the bill/makes sense. In this case, the following seems to pretty much cover it (from TFD):

number n

Usage Note: As a collective noun number may take either a singular or a plural verb. It takes a singular verb when it is preceded by the definite article the: The number of skilled workers is small. It takes a plural verb when preceded by the indefinite article a: A number of the workers are unskilled.

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As to why this might be, although not a grammatical or etymological explanation, it seems to me that in the first case it is the number that is the focus of the sentence. The sentence could be simplified to "the number is small" and still make sense. Whereas in the second case, it is the workers who are the focus of the sentence, and the simplified sentence would read "the workers are unskilled". If you said "the workers are small" it would have an entirely different meaning!

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I think that the same goes for:

group n

Usage Note: Group as a collective noun can be followed by a singular or plural verb. It takes a singular verb when the persons or things that make up the group are considered collectively: The dance group is ready for rehearsal. Group takes a plural verb when the persons or things that constitute it are considered individually: The group were divided in their sympathies.

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So to sum up, it seems that in both cases if it is the collective (number, group) that is the focus, a singular verb is used and if it is the individuals (workers, members of a group) that make up the collective are the focus, the plural verb is used.

Just adding my two penn'orth to RuthP's excellent explanation above.

I agree with the point you raise in your question, i.e. that this sentence could be read either way.

I don't think there is any way to determine which of the opposing meanings is intended as the sentence is written, (that the stable apex tone occurs in the basic motif, or that the failure to achieve a stable apex tone occurs in the basic motif), except perhaps I would be a tiny bit more inclined to think that the phrase which is placed nearest to the verb is the one meant, i.e. that the stable apex tone is what occurs in the basic motif.

However, with this unclear sentence construction I would not have very high confidence in that suggestion. I think if it was just changed as follows, that it would be clear:

The downward deflection to the A represents a failure to achieve a stable apex tone, such as occurs in the basic motif.

With this construction, I think it is clear that such as occurs ... refers to the stable apex tone, and not to the failure to achieve it.

There were a number of people on a bus stop.

The bus didn't arrive on schedule so they began to wonder, but had still some hope the bus would arrive soon.

After an hour or two there was a group of

I was going to say, hire a teenager to be your friend, perhaps some sloppy habits and sloth will rub off onto you, but seriously:

Agree with the posts suggesting that you have someone edit.

Also, be clear in your mind what you are trying to achieve. Have clear goals, once they are met, you should know when to put down the pen or step away from the keyboard. If your goals are unclear, then you'll always have a sense that the job may be incomplete.