Когда мы вошли в вагон, у окна было только одно свободное сиденье.

Because Когда мы вошли в вагон is a subordinate clause introduced by когда meaning when. In Russian, a subordinate clause is normally separated from the main clause with a comma.

So the sentence is structured like this:

• Когда мы вошли в вагон = when we entered the carriage
• у окна было только одно свободное сиденье = there was only one free seat by the window

Вошли is the perfective past form, so it presents the action as completed: we entered / we went in.

That fits this sentence because the speaker means:

• first, we entered
• then, they noticed there was only one free seat

If you used входили, that would be imperfective, which would sound more like:

• we were going in
• we used to go in
• we were in the process of entering

So вошли is the natural choice for a single completed event.

Because the subject is мы = we, and in the past tense Russian verbs agree with the subject in number (and in the singular, also gender).

For войти in the past tense:

• вошёл = he entered
• вошла = she entered
• вошло = it entered
• вошли = they entered / we entered

So мы вошли means we entered.

Because в can take different cases depending on the meaning:

• в + accusative = movement into
• в + prepositional = location in

Here there is motion: entered the carriage, so Russian uses в вагон.

Compare:

• Мы вошли в вагон. = We entered the carriage.
• Мы были в вагоне. = We were in the carriage.

Вагон usually means a railway car, train car, or carriage. Depending on context, English could translate it differently:

• train car
• carriage
• sometimes railcar

In this sentence, it most likely means a carriage or train car.

Yes, literally у окна means by the window or at the window.

In this kind of sentence, у is a very common way to say that something is located near something else. So:

• у окна = by the window / near the window

This is very natural when talking about seats, tables, doors, walls, and so on.

Because the preposition у requires the genitive case.

The base form is:

• окно = window

After у, it becomes:

• у окна = by the window

So окна here is the genitive singular form of окно.

Было is the past tense of быть in the neuter singular, and here it works much like English there was.

Russian often uses this kind of structure to introduce the existence of something:

• У окна было только одно свободное сиденье.
• literally: By the window there was only one free seat.

Also, сиденье is a neuter singular noun, so было matches it in form.

If the noun were plural, you would usually get были instead:

• У окна были свободные места. = There were free seats by the window.

Because сиденье is a neuter noun.

That means words agreeing with it must also be neuter:

• одно = one (neuter)
• свободное = free/vacant (neuter)
• сиденье = seat (neuter)

Compare:

• один свободный стул = one free chair (masculine)
• одна свободная скамья = one free bench (feminine)
• одно свободное сиденье = one free seat (neuter)

No. Here свободное means vacant, available, or unoccupied.

With seats, tables, rooms, and similar things, свободный often means that nobody is using it.

So свободное сиденье means:

• a free seat
• an available seat
• an empty seat

not a seat that costs nothing.

Только means only, and here it emphasizes the quantity:

• только одно = only one

So the idea is that there was just one free seat, no more than one.

The most natural reading is:

• было только одно свободное сиденье = there was only one free seat

Because Russian does not need a dummy subject like English there.

English says:

• There was only one free seat.

Russian simply uses the verb and the noun phrase, often with a location phrase first:

• У окна было только одно свободное сиденье.

So Russian expresses existence without adding an extra word equivalent to English there.

Yes. Russian word order is fairly flexible, but different orders change the emphasis.

This version is neutral and natural:

• У окна было только одно свободное сиденье.

It first sets the scene (by the window), then says what existed there (only one free seat).

You could rearrange it, but the emphasis would shift. For example:

• Только одно свободное сиденье было у окна.

This puts stronger focus on only one free seat, but it sounds more marked and less neutral than the original.

Yes, often место is very common when talking about available seats, especially in transport.

Compare:

• свободное сиденье = a free seat (the physical seat itself)
• свободное место = a free place/seat (often more general and very common in everyday speech)

So У окна было только одно свободное место would also be natural. The original sentence with сиденье simply focuses more specifically on the seat itself.