Avoiding screwing yourself out of a true 100% is very difficult (there are a lot of minor things you can do wrong that will cause you to lock yourself out of getting particular items and/or the abilities they teach, or certain Monster Bank entries). A few years ago I was working on a guide to this, but never finished it.
If all you care about is a 300-mission completion, though (which is all that the speedruns care about), it's much easier to avoid a mistake. All you need to do for that is to avoid discarding important mission items; the basic issue is that there isn't much of a clue in the game as to which are important, and the capacity is somewhat limited, making it very easy to discard an important item by mistake.
In case it helps, here's a guide to what can safely be discarded:
Can be safely discarded, and will be easily reobtained lategame if you discard it:
- Fire Sigil, Water Sigil, Wind Sigil, Earth Sigil
- Magic Trophy, Fight Trophy (note: do not discard Sport Trophy)
- Zodiac Ore, Mithril/Silvril (depending on translation), Materite, Leestone, Adamantite
- Jerky, Gyshal Greens, Telaq Flower
- Helje Key, Ancient Medal, Magic Cotton, Panther Hide, Encyclopedia, Rabbit's Tail
Can be safely discarded, but will be more difficult to replace if you do:
- Badge (note: this must be "Badge" alone, do not discard other items with "Badge" in their name)
- Mind Ceffyl, Body Ceffyl, Spiritstone
- Magic Cloth, Cyril Ice, Magic Vellum
Discarding any other mission item will lock you out of a full complement of that item permanently, and this has a high chance of permanently locking out some mission or other as a consequence. As far as I know, there's no intended way to lock yourself out of any mission unless you discard mission items. (There are online rumours that there's a glitch that permanently locks out "Free Bervenia!", but they differ in the details of what triggers the glitch, and as far as I know there's no confirmation that it actually exists. If you want to make sure, purchase and complete the mission as soon as it becomes available, making sure that you do not lose the resulting battle; this avoids every rumoured trigger for the glitch. There are comparable rumours related to "Left Behind"; the recommended way to avoid any issue here is to save before accepting it, to make sure that it's the only mission in the mission list when accepting it, and to complete its entire plotline before saving again. The plotline ends when you recruit a special character.)
There is also a mission called "Memories", which you're unlikely to come across at all (it's hard to get it to come up if you don't know what you're doing). This isn't a real mission, but rather unsets the "game complete" flag upon being accepted. If you do see it, I recommend not saving while the mission is accepted (if you accept it and then re-complete the game, the game simply just resets to your previous save file).
Also note that the "reserve missions" are intended to only be completable with the help of multiplayer. There is a 1 in 4 chance for any given save file that the reserve missions can be completed without trading; otherwise, you'll be stuck with some uncompleted missions as a consequence. These do not count as part of the 300-mission total, so won't lock you out of an all-missions completion.
