Learn Dutch: Er blijft geen enkele kruimel over.

Because kruimel is a de-word (de kruimel). When using the phrase geen enkel(e) to mean "not a single," you must add an -e to enkel if the noun is a de-word. If you were talking about a het-word, like het probleem (the problem), you would say geen enkel probleem.

What is the difference between saying geen kruimel and geen enkele kruimel?

Geen kruimel simply means "no crumb." Adding enkele makes the negation emphatic, changing the meaning to "not a single crumb." It stresses that absolutely zero is left.

Could I make the noun plural and say geen enkele kruimels?

No, geen enkel(e) must always be followed by a singular noun. This works exactly like English, where you say "not a single crumb" rather than "not a single crumbs."

Why does the word over appear at the very end of the sentence?

It is part of the separable verb overblijven (to remain / to be left over). In a standard main clause, the conjugated part of the verb (blijft) takes the second position, while the prefix (over) gets kicked to the end of the sentence.