If you enable the skip cutscenes option and skip the mandatory gondola cutscene during the gold saucer date, the outside of the gondola will be black. After saying a few lines, your date will then sit there and do nothing. Cloud will be completely unable to move or do anything and you will need to restart. You can skip the non-mandatory cutscenes if you wish though (the ones that you view when looking out of the window). The mandatory one has Cloud automatically look out of the window even if you dont touch the controls.
The save anywhere feature also breaks certain scenes where the party splits up. This can range from minor (e.g. after arriving in costa del sol, the party splits up and you can talk to them in town, if you use the PBS to put them in your party again, they all vanish from town and you miss the chance to talk to them) to game breaking (first time in gold saucer, when barret leaves and the rest are in the terminal, if you put the party members back in your party and talk to one of them, the other party members can get stuck on the stationery party member when exiting cloud's body).
Also, when you are rescueing Aeris from the Shinra building and need to sneak ast the soldiers guarding one of the floors, if you save during the "sneak past the guards" segment, cloud will be visible but tifa and barret will not be visible. They are still there and you can still get them to sneak past the guards, but since they are invisible its difficult to time their movements and signal them. They can still get caught by the guards in which case it will trigger a battle like normal.
Saving in the middle of the nibelheim flashback also causes you to get what is probably a corrupted save as the only party member listed will be cid and the save's location will be displayed as gibberish.
(not due to the game tweaks mod, but just thought i would put this here just in case)
If you use a save game editor or glitch to have Aeris in your party after the temple of the ancients, certain scenes will break because the game tries to play a scene for each party member, but doesnt know what to do when it finds Aeris. After the fight with JENOVA-LIFE, if you have Aeris in your party, she wont be visible as a party member, it will just be Cloud and your 3rd party member standing there. The scene then breaks because each party member is supposed to have a unique reaction at this point but the game doesnt know what to do with the Aeris party member. You will be frozen and unable to do anything except reload and replace Aeris with someone else for this battle.
