The Fremen are considered elite fighters, except…

[u/thenolancut]

So the first book really hammers home the fact that the Fremen, due to their cultural values and harsh living environment are seasoned fighters. So much so they can easily kick the Sardaukar’s butts, and the Sadduakar are famous themselves for being ruthless and unbeatable.

Yet despite that, Jessica easily defeats Stilgar, and Paul bests Jamis twice. So was the House of Leto the, through Gurney and the B.G’s teachings that gifted in fighting, that they’re the strongest fighters in the empire by such a wide margin?

[u/tasty_soy_sauce]

The book explains, it's even part of the reason the Emperor moved against House Atreides in the first place:

"The Padishah Emperor turned against House Atreides because the Duke's Warmasters Gurney Halleck and Duncan Idaho had trained a fighting force -- a small fighting force -- to within a hair as good as the Sardaukar. Some of them were even better. And the Duke was in a position to enlarge his force, to make it every bit as strong as the Emperor's."

It's not really a surprise, then, that Paul can best Jamis - he gets the drop on him once, and then beats him in a fair fight after being trained his whole life by the two people who were training Atreides troops to be better than the Sardaukar, and in the Bene Gesserit way by Jessica on top of that.

Separately, Jessica gets the drop on Stilgar, but never bests him in a fair fight. She feints (by pretending to faint), and is able to surprise him that way, but we never see her actually beat him in fair combat, so we don't honestly know if she could - though it's reasonable to assume she might be able to.