Na stole leży dwanaście flamastrów, ale zielony już nie działa.

Because na can take different cases depending on meaning:

• na + locative = location, meaning on
• na + accusative = movement onto something, meaning onto

Here the markers are already on the table, so Polish uses location:

• Na stole leży... = on the table lies...
• Compare: Kładę flamaster na stół = I put a marker onto the table

So na stole is correct because this sentence describes where something is, not where it is going.

Stole is the locative singular of stół.

The dictionary form is stół = table. After na in a location meaning, you need the locative:

• stół → na stole

The change may look a little irregular because ó often changes to o in related forms:

• stół
• stołu
• stole

This is just a normal stem change you will see in many Polish nouns.

Polish often prefers a position verb where English might just use is.

Here leży means is lying or lies. It tells you not only that the markers are there, but also that they are resting on the table.

Polish commonly uses:

• leżeć = to lie
• stać = to stand
• wisieć = to hang

So:

• Na stole leży dwanaście flamastrów sounds natural for objects lying on a surface.
• Na stole jest dwanaście flamastrów is possible, but it focuses more on existence/presence and sounds less specific.

This is one of the trickier parts of Polish numerals.

With numerals 5 and above, the whole phrase often behaves differently from an ordinary plural subject. In sentences like this, the verb is commonly singular.

So:

• dwa flamastry leżą = two markers are lying
• dwanaście flamastrów leży = twelve markers are lying

This is standard Polish grammar. A useful pattern is:

• 1 → singular
• 2, 3, 4 → plural
• 5 and more → noun in genitive plural, and the verb is often singular in this kind of sentence

So leży dwanaście flamastrów is normal and correct.

Because after numerals 5 and higher, Polish usually puts the counted noun in the genitive plural.

Compare:

• jeden flamaster = one marker
• dwa / trzy / cztery flamastry = two / three / four markers
• pięć / dwanaście flamastrów = five / twelve markers

So dwanaście flamastrów is exactly what Polish grammar requires.

Yes. Polish word order is more flexible than English word order.

This sentence starts with Na stole to set the scene first:

• Na stole leży dwanaście flamastrów...

You could also say:

• Dwanaście flamastrów leży na stole...

Both are grammatical, but the emphasis changes a bit:

• Na stole... emphasizes the location first
• Dwanaście flamastrów... emphasizes the quantity/item first

Polish often uses word order to manage focus and emphasis rather than strict grammar alone.

Because in Polish, ale normally introduces a new clause and is preceded by a comma.

So:

• Na stole leży dwanaście flamastrów, ale zielony już nie działa.

This is standard punctuation. It works much like English but when it joins two clauses.

Because the noun is left out, but it is still understood from context.

Earlier in the sentence we have flamastrów, so when Polish says zielony, it really means:

• zielony flamaster = the green marker

Polish often does this when the noun is obvious. English does something similar with the green one.

So:

• ale zielony już nie działa means
• but the green one no longer works

Because the missing noun is flamaster, and flamaster is masculine singular.

Adjectives in Polish must agree with the noun they describe, even when that noun is omitted.

So:

• zielony flamaster → masculine singular
• therefore just zielony = the green one

If the hidden noun were feminine, you would get zielona. If it were neuter, you would get zielone.

Już nie means no longer or not anymore.

So:

• działa = works / functions
• nie działa = does not work
• już nie działa = does not work anymore / no longer works

For a marker, this means it has stopped functioning properly, probably because it has dried out.

This expression is very common in Polish for objects, machines, devices, pens, apps, and so on:

• Telefon już nie działa = The phone no longer works
• Pilot już nie działa = The remote no longer works