U torbi su dvije bojice, ali plava bojica opet nedostaje.

Because u means in, and when it shows location, it takes the locative case in Croatian.

• torba = bag
• u torbi = in the bag

Compare:

• u torbi = in the bag, inside the bag already
• u torbu = into the bag, movement into it

So here it is u torbi because the crayons are located there.

Because su is an enclitic form of biti (to be), and Croatian enclitics usually go in the second position of the clause.

In U torbi su dvije bojice:

• U torbi is the first unit
• su comes right after it

So the word order is natural Croatian word order, especially in a sentence like In the bag there are two crayons.

You could also say:

• Dvije bojice su u torbi.

That is also grammatical, but it has a slightly different focus.

Because bojica is a feminine noun.

The numeral 2 changes for gender:

• dva for masculine and neuter
• dvije for feminine

So:

• dva auta = two cars
• dva sela = two villages
• dvije bojice = two crayons

Since bojica is feminine, dvije is the correct form.

After 2, 3, and 4, Croatian uses a special counting form of the noun.

So you get:

• dvije bojice
• tri bojice
• četiri bojice

For a learner, the easiest thing is to memorize that after dvije, the noun appears as bojice.

With this noun, bojice looks like the plural form, and it is exactly the form you use here. So dvije bojice is simply the correct phrase for two crayons.

Because the second clause is talking about one specific crayon: the blue one.

• dvije bojice = two crayons
• plava bojica = the blue crayon

So the sentence first mentions a group, and then it singles out one item from that context.

Because plava bojica is the subject of the verb nedostaje, so it must be in the nominative case.

• plava bojica = nominative
• plavu bojicu = accusative

You would use plavu bojicu in a sentence like:

• Tražim plavu bojicu. = I’m looking for the blue crayon.

But here the blue crayon is the thing that is missing, so it stays in the nominative:

• Plava bojica nedostaje.

Because adjectives in Croatian must agree with the noun they describe in:

• gender
• number
• case

Here the noun is:

• bojica = feminine
• singular
• nominative

So the adjective must match:

• plava bojica

If the noun changed, the adjective would change too:

• plavu bojicu (accusative singular)
• plave bojice (plural)

Because its subject is singular: plava bojica.

Even though the first clause talks about two crayons, the second clause is a separate idea:

• U torbi su dvije bojice = There are two crayons in the bag
• ali plava bojica opet nedostaje = but the blue crayon is missing again

So the verb agrees with plava bojica, not with dvije bojice.

Here nedostaje means is missing.

The verb nedostajati can mean:

• to be missing
• to be lacking
• sometimes even to be absent

So:

• Plava bojica nedostaje = The blue crayon is missing

This is a very natural Croatian verb for this idea.

Opet means again.

So:

• plava bojica opet nedostaje = the blue crayon is missing again

It tells you this is not the first time it has happened.

Its position is fairly natural here, before the verb:

• plava bojica opet nedostaje

Croatian allows some flexibility, but this placement sounds normal and clear.

Because Croatian does not have articles like English a/an/the.

So bojica can mean:

• a crayon
• the crayon

The exact meaning comes from context.

Here plava bojica is understood as the blue crayon because the context makes it specific.

Because ali means but, and in Croatian it normally introduces a new clause. A comma is standard before it.

So:

• U torbi su dvije bojice, ali plava bojica opet nedostaje.

This is the normal punctuation.

Yes. Croatian word order is flexible, so other versions are possible, for example:

• Dvije bojice su u torbi, ali plava bojica opet nedostaje.
• U torbi su dvije bojice, ali opet nedostaje plava bojica.

These are grammatical, but the original sentence is very natural. The original word order gives a smooth, neutral flow and keeps the focus clear.