Pensé que estabas enfadada conmigo, pero solo fue un malentendido.

Pensé is the preterite of pensar, and here it means I thought at a particular moment in the past.

• Pensé que... = I thought that... / I assumed that...
• Pensaba que... would sound more like I used to think... or I was thinking..., depending on context.

So:

• Pensé que estabas enfadada conmigo = at one moment, I got the idea that you were angry with me.
• Pensaba que estabas enfadada conmigo = I had that belief for some time, or that was my ongoing impression.

Because estar enfadada describes a state or condition, and in this sentence that state is seen as ongoing/backgrounded in the past.

• estabas enfadada = you were angry
• estuviste enfadada = you were angry too, but it sounds more like a completed, bounded period of time

After Pensé que..., Spanish often uses the imperfect to describe what someone seemed to be feeling or being at that time:

• Pensé que estabas cansada
• Pensé que estabas enfermo
• Pensé que estabas enfadada

So estabas fits the idea of what I believed your state was.

Because adjectives in Spanish must agree with the person they describe.

Here, enfadada describes you (tú), and the speaker is talking to a female.

• to a woman: estabas enfadada
• to a man: estabas enfadado

So the ending changes to match gender.

Yes — enfadado / enfadada is a very common way in Spain to say angry, annoyed, or upset.

It can range from mildly annoyed to properly angry depending on context.

In Spain:

• enfadado/a = very natural, standard
• enojado/a = understood, but more common in many Latin American varieties than in Spain
• cabreado/a = also common in Spain, but more colloquial and stronger

So for neutral everyday Spanish from Spain, enfadada is a great choice.

After a preposition like con, Spanish uses a prepositional pronoun, not a subject pronoun.

So:

• yo becomes mí
• but with con, Spanish uses the special form conmigo

Examples:

• para mí
• sin mí
• de mí
• but conmigo

Similarly:

• contigo = with you
• consigo = with himself/herself/themselves (in certain contexts)

So enfadada conmigo means angry with me.

Because Spanish normally needs que to introduce a subordinate clause after verbs like pensar, creer, decir, saber, etc.

So:

• Pensé que estabas enfadada conmigo
• literally: I thought that you were angry with me

In English, that is often omitted:

• I thought you were angry with me

But in Spanish, omitting que here would sound wrong.

Because Spanish often leaves out subject pronouns when the verb ending already makes the subject clear.

• Pensé already tells you the subject is I
• estabas already tells you the subject is you (informal singular)

So:

• Pensé que estabas enfadada conmigo
  is more natural than
• Yo pensé que tú estabas enfadada conmigo

You can include yo or tú for emphasis, contrast, or clarity, but they are not usually needed.

Here fue sounds more natural because the speaker is identifying what the situation turned out to be.

• fue un malentendido = it was just a misunderstanding
• It presents the misunderstanding as a complete event/explanation.

Using era is not impossible in some contexts, but it would sound less natural here because era usually gives background description, while fue gives the conclusion or result.

Compare:

• Al final, fue un malentendido. = In the end, it was a misunderstanding.
• Era un malentendido = It was a misunderstanding.
  This can work, but it feels more descriptive and less like a resolved conclusion.

Malentendido means misunderstanding.

It comes from:

• mal- = badly / mis-
• entendido = understood

So the literal idea is something like something understood badly/wrongly.

It is a very common noun:

• Fue un malentendido.
• Todo fue un malentendido.
• Hubo un malentendido entre nosotros.

In modern standard Spanish, solo is usually written without an accent, even when it means only.

So this sentence is normally written:

• pero solo fue un malentendido

Older usage, or some writers for clarity, may use sólo, but current standard spelling generally prefers solo unless there is real ambiguity.

So for learners, the safest default today is:

• solo = standard spelling

Yes. The structure is very reusable:

• Pensé que estabas enfadada conmigo = with me
• Pensé que estabas enfadada con él = with him
• Pensé que estabas enfadada con ella = with her
• Pensé que estabas enfadada con nosotros = with us

So the pattern is:

Pensé que + imperfect of estar + enfadado/a + con + person

Yes, and it is very similar, but there is a slight nuance.

• Pensé que estabas enfadada conmigo = I thought you were angry with me
• Creí que estabas enfadada conmigo = I believed / thought you were angry with me

Creí can sound a little stronger, as if you genuinely believed it to be true.
Pensé can sound a bit more like I got the impression or I assumed.

In everyday speech, both can work here.

Yes, a little. The original sentence is very natural:

• Pensé que estabas enfadada conmigo, pero solo fue un malentendido.

You could also hear:

• Pensé que estabas enfadada conmigo, pero fue solo un malentendido.
• Pensé que estabas enfadada conmigo, pero al final fue un malentendido.

The original version places solo before fue, which sounds very natural and emphasizes that it was just a misunderstanding.

So the exact word order can vary, but the original sentence is perfectly idiomatic.