You mean what are the worst/hardest/most annoying missions in the game? Well.
Considering equal-level and decent equipment, Altera 5th, because it can get pretty tough on hard/very hard, what's with the factories. Alera Core on Very Hard, as it is just TOO DAMN LONG. I'd say Peyita 4th, because if you don't know about the boss, you're fucked. Peyita 5th and 6th, because the bosses are complete whores (5th, "Cuttersark", is pretty hard to hit and fast, already told you guys about barud,) and peyita 6th you gotta fight all minibosses from peyita (Let's see, that would be the High Gullito Magician, whose attacks cause curse, which lowers MP, High Gullito Archer, which is pretty much Ezio Alditore and Altair from Assasin's Creed + Bow, and his attacks poison. And the High Gullito... Hammerer? Dunno, but in P5 he's easy and abusable, not so much on 6th, he is rather fast, but thankfully doesn't hit very hard.).
Then, Velder, pertty much the entirety of Velder, with the only exception beyond Velder 2nd, and only if you're a Rune Slayer (PHOENIX TALON SPAM FOR THE FUCKING WIN), with very, VERY special emphasis on the last three, Velder 4th is unpredictable, can easily put you on fire, summons freaking dolls, and can enter a "rampage" mode, that makes him 5x faster for roughly a minute. Velder 5th is annoying, what's up with all of these pits and dragon-spam? And the gooddamned boss, he just has a 3-hit attack that barely deals damage, and a "trap" attack that stops your movement, but there are "portals" that appear on the field, if they stay alive for long enough, they create a dark field, the boss will enter the field, and unleash attacks that come from exactly where you are standing, hit about 4 times for 11k damage each, and the accurse "Black Hole", which has infinite-range and has about 5x the suction power from Eve's "Generate Black Hole", it hits you for 5k damage for about 40 times, and ends in an explosion for about 40k damage, the math says 240k damage, and he loves to spam it. I've told you guys about the Dark Nephirim.
As for Hamel, can't say much about it, as I've only played Hamel 1, but Hamel 3 seems to be annoying as the boss seems to multiply.