What is the difference between "Hept-" and "Sept-" prefixes?

It's the difference between Latin and Greek. Four, five and six do have their own forms.

Latin: bi-, tri-, quad-, quin-, sex-, sept-...
Greek: di-, tri-, tetra-, pent-, hex-, hept-...

Generally, Latin prefixes are added to Latin roots and Greek prefixes to Greek roots.

Quadrilateral, quintuplet, September etc.;
Tetrahedron, heptagon etc.

The Greek and Latin numeral words are cognates. That means they come from the same source (Lat co-gnatus 'born together').

In particular, they come from Proto-Indo-European, the parent language (dating from around -3000) of modern European languages (excepting only Basque, Finnish, Estonian, and Hungarian).

See this page for details about the derivations of European numeral words. (You'll probably have to rotate it; it's a pdf scan in landscape mode)

"Hept-" is from the Greek "hepta". (See, for example, the Online Etymology Dictionary entry on "heptagon".)

And we do see this distinction with other numbers (though a number of Greek and Latin number terms are cognate). A tetragon, for example, is a four-sided polygon. We also speak of "pentagons" and "quintuplets".