Magistra vult discipulos non solum tabellas in capsam deponere, sed etiam ea quae audiverunt inter se conferre.

Because discipulos is the subject of the infinitives deponere and conferre, not the subject of vult.

With vult, Latin often uses this pattern when one person wants someone else to do something:

• magistra vult = the teacher wants
• discipulos ... deponere / conferre = the students to put down / to compare

So this is the common accusative + infinitive construction:

• Magistra vult discipulos laborare = The teacher wants the students to work

Here, discipulos is understood as the doer of both infinitives.

They are infinitives because they express the actions that the teacher wants the students to do.

English uses to:

• wants the students to put
• wants the students to compare

Latin usually does not need a separate word like English to. The infinitive ending itself carries that idea:

• deponere = to put down
• conferre = to bring together / compare / discuss

So the structure is basically:

• Magistra vult discipulos ... deponere ... conferre
• The teacher wants the students ... to put down ... and to compare

This is a very common pair meaning not only ... but also.

In this sentence it connects two infinitive phrases:

• non solum tabellas in capsam deponere
• sed etiam ea quae audiverunt inter se conferre

So the sense is:

• not only to put the tablets into the box, but also to compare/discuss what they heard with each other

It is a neat way of showing that two actions are being required, with the second added as an important extra.

It goes with both.

Latin often states the accusative subject once and lets it apply to multiple infinitives if the sense is clear. So discipulos is the understood subject of both:

• discipulos ... deponere
• discipulos ... conferre

In English, we also often avoid repeating the noun:

• The teacher wants the students to do X and Y

rather than:

• The teacher wants the students to do X and wants the students to do Y

Because in with the accusative usually shows motion into something.

So:

• in capsam = into the box
• in capsa = in the box or inside the box as a location

Since the action is one of placing something into the box, the accusative is used.

This is a very important Latin distinction:

• in
  • accusative = movement into
• in
  • ablative = position in

It means the things which they heard or more naturally what they heard.

Break it down like this:

• ea = those things / the things
• quae audiverunt = which they heard

So together:

• ea quae audiverunt = the things that they heard

Here ea is useful because Latin often uses a neuter plural pronoun to mean things in a general sense.

Because it agrees with ea.

• ea is neuter plural
• so the relative pronoun must also be neuter plural: quae

Its case comes from its job inside the relative clause. In quae audiverunt, quae is the object of audiverunt, so it is accusative plural neuter.

So:

• gender and number: from ea
• case: from its role in quae audiverunt

This is a standard rule for relative pronouns in Latin.

Because the hearing happened before the comparing/discussing.

The students are supposed to compare the things they have heard. So first they heard them, and then they compare them.

The perfect here can often be translated in English as either:

• they heard
• they have heard

depending on context.

In this sentence, English might naturally prefer what they heard or what they have heard.

Inter se means among themselves, with each other, or one with another.

• inter = among / between
• se = themselves

So inter se conferre means that the students are comparing or discussing things with one another, not with the teacher.

This is a very common Latin expression for reciprocal action.

Because Latin uses the reflexive pronoun se to refer back to the subject of the clause.

Here the understood subject of conferre is discipulos, so se refers back to them:

• discipulos ... inter se conferre = the students ... compare among themselves

If Latin used eos, that would point to them as some other group, not reflexively back to the students themselves.

So inter se is exactly right for with each other.

Its basic literal sense is indeed to bring together, but in context it often develops into meanings like:

• compare
• discuss
• exchange
• contribute, in other contexts

With inter se, the idea is that people bring their thoughts together, so the phrase commonly means to compare with each other or to discuss together.

So here ea quae audiverunt inter se conferre means something like:

• to compare what they heard with each other
• to discuss among themselves what they heard

Yes: the word order helps show the parallel structure.

After vult, the sentence is arranged in two balanced parts:

• non solum tabellas in capsam deponere
• sed etiam ea quae audiverunt inter se conferre

Each part has:

• an object
• then the rest of the phrase
• then the infinitive

Latin word order is flexible, but this arrangement makes the contrast and balance very clear. It also helps the reader hear the not only ... but also pattern more strongly.

So the order is not random; it supports the sentence’s structure and emphasis.