The game can crash in several consistent spots, especially on the GameCube version, so I'm going to go over the methods that I've found to reliably prevent and replicate most of them.

• Onua Crash/Rahi Shield Crash: Do NOT use your shield while touching hoto bugs or nui-jaga. 100% avoidable, only occurs on GC. Shielding while touching either of these enemies will play a special SFX, and having this happen more than a few times will cause the game to freeze at the next load zone. This was pretty frequent in Onua due to hoto spawning around the 1st and 3rd pushable rocks, so instead of shielding just take the hit from them and use the i-frames to push through. This crash can also happen in Tahu Mata, Gali, and Takanuva. This will not occur when shielding other enemy types, enemies in Kopaka, and for some strange reason Stanley (the first nui-jaga in Tahu Mata) Example:
• Pohatu End Crash: Don't mash jump in the tight hallways or during the final segment. That's about it. Doing this loses a few frames anyways.
• Kopaka Tunnel Crash: Prevent the camera from bugging out during the ice tunnel by not going too far right. If you hug the very right side of the ice tunnel during the timed section, the camera will usually bug out for a moment and the game can very rarely crash shortly after. Try to ride the right side of the ridge on the ground and you should avoid the camera bug while not compromising your cornering speed too much. Example of the camera bug and crash:
• Kopaka End Crash: Don't mash buttons after the final cutscene and before "level complete" appears. The game gives you just under 1s to control Kopaka between the final cutscene and the level complete trigger. Moving or jumping seem to trigger this more often so avoid mashing your menuing inputs too early. Example where I mash Up/A too early and crash:
• Gali Splash'n'Crash: Avoid splashing too much against a wall, GC only. This has a consistent setup to intentionally trigger it, but afaik it has only ever been unintentionally triggered twice in a different spot so it's not really something to worry about. Swimming into a sloped wall close to the water surface can cause Gali to repeatedly splash. If you splash either too much or at a very specific swim height, the game will crash. Example: