Rock-paper-scissors (aka Janken, San-sukumi, etc.), is an umbrella term for the ways systems can collide. Just like the actual game they refer to (rock beats scissors, scissors beats paper, paper beats rock), there are three options stacked so that there is an expected winner and an expected loser.
In fighting games, this is extremely basic. It takes several forms, not all of which apply to every game. The following are concrete examples:
A striking attack can be blocked, but someone who is blocking can be thrown. Someone who is attempting to throw can be struck.
Zoning against the ground is weak to jumps, but jumps can be picked out of the air with an anti-air move. However, anti-air moves are generally weak to zoning.
Strikes will be caught by traps, but traps are susceptible to throws.
Air-blocking can keep jump attacks in check, but it is vulnerable to an air throw. However, an air throw can get smashed by a jump attack.