Episode 1, Any Difficulty, Ruins 1
You see a huge hole and a waterfall, right Behind the waterfall, you will see a pathway there. What's there is just some boxes. People think it's a glitch but it's really a secret passage way.
If you are playing the quest TTF (Towards the Future): Only if you have the weapon "Branch of Paku Paku" (Force Weapon). There should be a secret teleporter in the hospital (usually I call it the "infirmary") and you gain access to Ruins. Go behind the waterfall, a popular character, Chao will talk to you. If he says he wants to join you... Say yes. Your "Branch of Paku Paku" will become "Striker of Chao", your Shifta and Deband range will be doubled. Also adorable. :3
Episode 2, Any Difficulty, Seabed Lower Level (After Seabed Higher Level)
You will happen to be in a room where water leaks and glass on the floor. There is a passage way on your left and you should able to pass through. Sometimes there's boxes or a healing ring. And if you turn around you might encounter a Sinow Zele (sometimes, depends on what map you are playing).
If you are playing the quest RT (Respective Tomorrow): As you enter a room with Reco Boxes on your left, just go to the path where there used to be a door. You will walk through it. There you will find boxes and a red switch. You will unlock the red gate in the secret passage way I explained. However, that only leads to a healing ring room. You might sometimes enter Tower, only if you got a random message during Seabeds (Lower) then you might have an access to Control Tower and you cannot fight Olga Flow at the end for some reason and I'm sure you will.
*Please PM me about the "Striker of Chao" in TTF or Access to Towers in RT for more details. This is completely off topic. :P