Many ways to add difficulty to a game.
Increase the number of enemies or obstacles.
Increase the speed and artificial intelligence of enemies.
Make player handicapped with less ammo or reduce number of health restore items.
Change the scenery using lighting effects. Make the player play the levels in the dark, rain, snow etc.
Make jumping platforms farther apart and make obstacles they have not seen to slide under or crawl up.
create puzzles like switches or keys to find and make those harder to solve in harder levels.
Change the physics of the player. Make them fly through a level or skateboard or hop or take away gravity.
Just a few ways to add difficulty to a level.