I bought a couple of these up a year or so back when I went through the metal gear series and dedicated a thread to it, but the original Metal Gear is full of these. I'll list a few in no particular order.
-Elevators go one direction only. If you get on an elevator and go past the floor you wanted to get off on, you have to go to the other elevator(which might be on the far side of the building, past traps and guards) to go back the other direction and get off at the right floor. The first building is 4 or 5 floors tall, so this will happen at least once. There is no stated reason that the elevators work like this except maybe that Big Boss is a massive dick.
-There are many locked doors that require keycards to open and 9 levels of key cards to collect across the game. The doors have no indication which keycards open them and there's no rhyme or reason to how they're placed, so a level 9 door might be followed by a level 2 door and the only way to find out is to walk up to a door, equip a keycard and keep doing that until the door opens.
-You can only have one item equipped at a time. This includes your gas mask and if you don't have it equipped, it doesn't work. Keep that in mind when I say there are numerous rooms with poison gas which slowly deplete your health and have locked doors. Remember what I wrote above about the key cards and doors? Now imagine having to unequip your gas mask to cycle through every keycard you have in a poison gas room hoping you figure out which card opens the door before you lose too much health because Snake apparently can't wear a gasmask and hold a keycard at the same damn time.
-There are POWs across the game you must rescue. Well, technically you don't have to rescue them but your rank increases after you rescue X number of POWs and that determines how much health you have and ammo you can carry. Even better, you can LOSE a rank each time you kill a prisoner, accidental or not. There's a boss near the end of the game who has 3 POWs around him and it's difficult to kill him without killing one of the POWS, so you're almost expected to lose a rank. Did I mention the number of POWS are finite and there's enough to maybe regain rank once if you kill a prisoner?
-To top off this shit sundae, the Metal Gear fight at the end is a fucking joke, but a bad one. So you don't actually fight the Metal Gear. The Metal Gear stands there in it's hanger and you place 16 bombs on it's legs in a precise order while some lasers fire at you from above. The problem is because of the whole "Lose rank" problem, it's possible to lose a couple ranks and literally not be able to carry enough bombs to complete this fight. And even better, if you fuck up the order, you need to start again. And fnally, someone does give you the order, all up until the final bomb, so you have a 50-50 chance of getting the last bomb on the correct leg.
The bright side is, Kojima learmed from Metal Gear, as you'll probably notice a lot of these problems aren't in later Metal Gear games. Even by Metal Gear 2, the keycard issue had been greatly simplified, the rank system vanished, the prisoner rescues because plot progression and the elevators have UP and DOWN buttons.