i should probably clarify a bit more, specifically the fight with 5 hyenas before you even get the disc, if you have used the hamburger already and saved (which i did on my first run cause i had some bad luck in the very first hyena encounter) that fight becomes much more difficult and dependent on hyenas dying fast enough with hard knocks (since at least in my expirence the base attack is too slow for that fight that early on) or the hyenas missing. It's not really a tough fight per-se it's just easy to accidentally make it a much harder fight. and once you realize about the item management part there's no way to go back without starting an entirely new file and then replaying the first section again. It's not the end of the world of course but it's certainly stinks to get stuck in the part of the game before anything sexy happens and have to start a new file be the best solution.
Ah pardon then, I thought you were talking about the fights near the end. Yeah, saving with the wrong timing could give you trouble there, but only if you're not rotating saves, which is pretty much standard practice for any challenging and unpredictable game. If you didn't have a save right at the beginning of the Barrens, you should have at least had one in Haven as you were preparing to leave, which is only a few minutes difference. If you were playing the whole game on one save...well, now you've learned your lesson. And really, GT is a lot less punishing on that front than a lot of games.