syatu ni koohii no simi ga tukimasita.

A natural way to break it down is:

• シャツに = on the shirt / to the shirt
• コーヒーのしみ = a coffee stain
• が = marks coffee stain as the thing being talked about grammatically
• つきました = got on / got attached / appeared on

A very literal reading is:

• A coffee stain got on the shirt.

This is a very normal Japanese pattern:

• [place] に [thing] が つく

meaning something gets onto / attaches to a place.

Japanese often leaves out information that is obvious from context.

In English, we usually say my shirt, but in Japanese, if it is already clear whose shirt it is, just saying シャツ is enough.

So:

• シャツにコーヒーのしみがつきました。
  = There’s a coffee stain on my shirt / The shirt got a coffee stain, depending on context.

If you really need to make it explicit, you can say:

• 私のシャツにコーヒーのしみがつきました。

But in everyday Japanese, that often sounds more explicit than necessary.

Here, に marks the place where something ends up.

In this sentence, the stain got onto the shirt, so シャツに means:

• on the shirt
• to the shirt

This is different from English, where we often just use on. In Japanese, verbs like つく often use に with the location.

Compare:

• 服に汚れがついた。 = Dirt got on the clothes.
• 手にインクがついた。 = Ink got on my hand.

So に is the natural particle here.

の connects two nouns. Here it shows what kind of stain it is.

So:

• しみ = stain
• コーヒーのしみ = coffee stain

You can think of it as:

• a stain of coffee
• a coffee stain

This use of の is very common:

• 水のボトル = water bottle
• 日本の会社 = Japanese company / company of Japan
• チョコレートのケーキ = chocolate cake

So in this sentence, コーヒーの describes しみ.

Because しみ is not the direct object here. It is the thing that got on the shirt.

The verb つく is intransitive, so it does not take を in this pattern. Instead, the thing that appears or attaches is marked with が.

So:

• コーヒーのしみがつきました
  = A coffee stain got on (it).

If you used を, you would need a transitive verb instead, such as つける:

• コーヒーのしみをつけました。
  = (Someone) put/made a coffee stain.

So:

• つく → intransitive → が
• つける → transitive → を

つきました is the polite past form of つく.

In this sentence, つく means something like:

• to stick
• to get on
• to attach
• to come onto

So しみがつきました means:

• a stain got on it
• a stain appeared on it
• it got stained

This is a very common verb for stains, dirt, smells, and similar things:

• 汚れがつく = to get dirty / to get a mark on it
• 傷がつく = to get scratched
• においがつく = to get a smell on it

This is a very common point in Japanese.

The past tense here does not necessarily mean the stain is gone now. It means the change happened: the shirt got a stain.

Japanese often uses the past tense to describe a completed change of state.

So:

• しみがつきました = a stain got on it
• The result may still be true now.

English often switches to a present-state expression like:

• There’s a coffee stain on my shirt.

Japanese can also describe the resulting state in other ways, but つきました is perfectly natural when focusing on the event of getting stained.

This is the classic intransitive/transitive pair:

• つく = something gets attached / gets on
• つける = someone attaches something / puts something on

So:

• シャツにコーヒーのしみがつきました。
  = A coffee stain got on the shirt.

But:

• シャツにコーヒーのしみをつけました。
  = (Someone) put/got a coffee stain on the shirt.

The first sentence focuses on the stain appearing on the shirt.
The second suggests an agent, even if the agent is not named.

For accidental situations, Japanese often prefers the intransitive version unless you specifically want to say who caused it.

Yes, but it changes the nuance.

The original sentence with が is a straightforward statement about what happened:

• シャツにコーヒーのしみがつきました。

If you use は, you are usually making a topic or contrast:

• シャツにはコーヒーのしみがつきました。
  = As for the shirt, it got a coffee stain. / The shirt, at least, got a coffee stain.

This can sound contrastive, like maybe something else did not get stained.

You could also say:

• シャツにコーヒーのしみはつきました。

but that sounds more marked and context-dependent.

So for a simple neutral statement, the original version is the most natural.

Yes, and it means something slightly different.

• シャツにコーヒーがつきました。
  = Coffee got on the shirt.

This focuses on coffee itself getting on the shirt.

• シャツにコーヒーのしみがつきました。
  = A coffee stain got on the shirt.

This focuses on the stain/mark left by the coffee.

So the original sentence is more specific: not just that coffee touched the shirt, but that it left a visible stain.

They are related, but not exactly the same.

• しみ = a stain, blotch, mark that has soaked in or is hard to remove
• 汚れ = dirt, filth, grime, general stain/soiling

So a コーヒーのしみ is specifically a coffee stain.
If you said 汚れ, it would sound more general:

• シャツに汚れがつきました。
  = The shirt got dirty / got a mark on it.

So しみ is the better word when you want to emphasize the stain itself rather than general dirtiness.