В магазине лежали кекс с изюмом, рулет с яблоком и торт с белой глазурью.

Because after в meaning in, Russian uses the prepositional case for location.

• магазин = store, shop
• в магазине = in the store

So this is a standard location pattern:

• в доме = in the house
• в школе = at school
• в магазине = in the store

If в meant motion into, you would usually see the accusative instead.

Because the subject is really a list of three things:

• кекс с изюмом
• рулет с яблоком
• торт с белой глазурью

Each noun is singular by itself, but together they form a plural subject, so the verb is plural:

• лежали = they were lying / were sitting / were there laid out

If there were only one item, you would use singular, for example:

• В магазине лежал кекс с изюмом.

Лежать literally means to lie. In Russian, it is often used for objects that are physically lying somewhere or laid out somewhere.

So в магазине лежали... suggests the pastries were physically there, probably on a counter or shelf.

Compare:

• были = were, existed
• лежали = were lying, were laid out

Russian often prefers a more concrete verb than English does. English might just say there were, but Russian naturally says лежали, стояли, висели, etc., depending on position:

• книги лежали на столе = the books were lying on the table
• бутылки стояли на полке = the bottles were standing on the shelf
• картина висела на стене = the picture was hanging on the wall

They are in the nominative singular, because each one is part of the subject of the sentence.

Even though the whole subject is plural as a group, each item named in the list is still a single object:

• кекс
• рулет
• торт

This is similar to English: A muffin, a roll, and a cake were on the table. Each noun is singular, but the whole set is plural.

Because the preposition с meaning with normally takes the instrumental case.

So:

• изюм → с изюмом
• яблоко → с яблоком
• белая глазурь → с белой глазурью

This is one of the most important uses of the instrumental case in Russian.

A few similar examples:

• чай с сахаром = tea with sugar
• бутерброд с сыром = sandwich with cheese
• девушка с книгой = a girl with a book

Because both the noun and the adjective must be in the instrumental case after с.

Base form:

• белая глазурь = white icing

After с:

• с белой глазурью

Both words change:

• белая → белой
• глазурь → глазурью

The adjective has to agree with the noun in:

• gender
• number
• case

Since глазурь is feminine singular instrumental, белой must also be feminine singular instrumental.

In food descriptions, Russian often uses the singular to name an ingredient or filling in a general way.

So:

• рулет с яблоком means something like a roll with apple filling / with apple

This does not necessarily mean there is exactly one whole apple inside. It is just the normal way to name the flavor or ingredient.

The same thing happens in many food phrases:

• пирог с мясом = meat pie
• булочка с маком = bun with poppy seeds
• мороженое с шоколадом = ice cream with chocolate

Sometimes plural is possible in other contexts, but here singular is the most natural way to label the pastry.

Russian word order is more flexible than English word order, but different orders can sound more natural in different contexts.

Starting with В магазине sets the scene first:

• In the store, there were...

This is very natural if the sentence is introducing what was present there.

The sentence could be reordered, but the emphasis would shift. For example:

• Кекс с изюмом, рулет с яблоком и торт с белой глазурью лежали в магазине.

This is grammatically fine, but it sounds more like the baked goods are the main topic, and only then do we say where they were.

So the original order is natural for presenting the location first.

Usually no, not in this exact sentence, unless the speaker wants a different physical image.

• лежать = to lie
• стоять = to stand

Cakes and pastries on a shelf, tray, or counter are often conceptualized as lying rather than standing, so лежали is the more natural choice here.

That said, Russian sometimes chooses these position verbs a bit differently from English, and context matters. But for baked goods laid out in a shop, лежали is very normal.

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

So:

• кекс can mean a muffin/cake or the muffin/cake
• торт can mean a cake or the cake

Whether the meaning is indefinite or definite depends on context, word order, and the situation.

That is why a Russian sentence can look more compact than its English translation.

Usually yes, or at least physically present in a way that suggests placement.

Because лежали is a concrete positional verb, it gives a more visual picture than a plain existential verb would. It suggests the items were somewhere in the store as objects lying there, likely on a counter, shelf, or display.

So the sentence does not just tell you the items existed in the store. It helps you picture them there.