Mdtryhht

I came across this sentence:

We thought that Joe didn’t go to the museum with the rest of the class.

The Manhattan Sentence Correction Guide says it’s an incorrect construction and it should be:

We thought that Joe hadn’t gone to the museum with the rest of the class.

What is wrong with the first one?

Neither is incorrect, but the first one is markedly unusual, whereas the second one is very natural.

Both sentences are written in the past tense, but the second uses the perfect construction. The perfect changes what the reference point is. In this example it means that at the time when we were doing the thinking, our thoughts were about the past. If I was speaking in the present I could say

We think that Joe didn't go to the museum with the rest of the class.

To refer to this thought afterwards we shift both verbs. Think is in the present so we turn it on the past thought, but didn't go is already in the past, so we turn it into the past perfect hadn't gone.

The first sentence is more unusual. If we consider what its corresponding present tense version would be, we can see that it would be describing a habitual situation:

We think that Joe doesn’t go to the museum with the rest of the class.

This is a pretty weird non-habit to be commenting on, so although it is a grammatical possibility, it's unlikely to have been what was meant.

The previous answer by @curiousdannii is right to note that both forms are acceptable here.

In fact "we thought that" can be considered a form of indirect or reported speech (a variant of 'they said that') and if you examine what the direct speech form would have been, you can make sense of this sentence:

It could have been

We thought, "Joe doesn't go to the museum"

When this is written as reported speech, it becomes

we thought that Joe didn't go to the museum

where 'doesn't' is converted into 'didn't' for the tense to be in agreement with the past tense form 'we thought.'

Now, what if the original sentence was

we thought, "Joe didn't go to the museum"

This is where the style guide might be putting the tense an extra degree into the past, from 'didn't' (simple past) to 'hadn't' (past perfect) as in

we thought that Joe hadn't gone to the museum.

However, it is not necessary, because 'didn't' already agrees with the past tense of 'we thought' and the strict rule of past perfect in terms of which event occured earlier is not relevant here, because this is a form of reported speech. So it is just as correct to write

we thought that Joe didn't go to the museum

or even

we had thought that Joe didn't go to the museum

although that sentence would need to be understood in its own time context depending on what comes before and what follows.

Most grammar books try to explain the English tenses as if they were mathematical formulas - there's correct and there's not.

The problem is that the English tenses (and the English grammar, in general) are not mathematical formulas, and many times more than one tense fits the context.

there are cases where some specific tense is simply wrong for a specific context, like

I haven't seen her last week

we don't use the present perfect tense with a finished time period. not because it's "incorrect" but merely because it doesn't make any sense: the present perfect has many roles, discussing some action in some finished time period isn't one of them.

But this is a very specific case, and many times, it's not about "what's right" or "what fits here better" but it's more about "what do I want to emphasize"?

the Past Perfect emphasizes (among other usages) the fact that one action had finished (or hadn't finished) before another action in the past. the keyword here is emphasizes.

Don't look at me. the house had been a mess way before I got here.

in this case, I want to emphasize the fact the messiness of the house existed before I got there. I used the Past Perfect.

Usually, we can understand from the context what happened before what, and emphasizing the order of them is just redundant, or the order doesn't matter to begin with.

We thought that Joe didn’t go to the museum with the rest of the class.

Here, it's kind of obvious we though about Joe after he went (or didn't go) to the museum, and also, we don't care to much if our thinking happened before he went to the museum, it doesn't really matter here.

when more than one tense fits the context, think what you want to emphasize. when you hear a speaker speaks, think what he or she wants to emphasize by their tense choosing.

What's wrong with the first one ("We thought that Joe didn’t go to the museum with the rest of the class") is that in most contexts, the going to the museum happened farther in the past than the thinking. In English, you indicate this by making sure that the more remote action is a more remote tense. "Had gone" is older than "thought."

It is possible to construct a context in which the sentence as written is the best fit. But most of the time the simple timeline approach that I outlined will stand you in good stead.

I agree with John Lawler‘s comments. The way English is taught is often too technical and demanding adherence to strict rules. What is virtually never discussed is that there is a literary standard speech in English and a colloquial style, which probably is used more often than not by native speakers without them even knowing it. Contrasting the two sentences, someone should have pointed out in the book, that the former was colloquial English (not „wrong“ or „bad“ grammar, which native English speakers never use) and that the latter was the literary standard. An elevated style perhaps. They are both correct. To call the latter „better English“ and the former „bad“ English is just a meaningless value judgment. Native speakers frequently do not use the past perfect tense, often because it‘s unnecessary based on the context. English learners need to be taught this, but almost never are. There are some grammar errors no native speaker ever makes and non-natives do make. Those needed to be highlighted and corrected. „If you have to be taught something about your native language, the odds are about 100% that what you are being taught is wrong. Otherwise you wouldn‘t have to be taught it. And, you have to be taught it because it‘s NOT your language. In fact, it often can‘t even be part of any language.“ Noam Chomsky,PhD, 1989 interview, Professor Emeritus in Linguistics, MIT.