As a hacker:
Forgetting to create a back-up: Self-explanatory, this usually costs me hours and hours of time I could have used to add more content
Good sprites that are terrible in-game: It's sort of annoying to find out the sprite I've been working on for hours on end happens to have wonky colors or disproportional body parts when compared to other sprites.
Broken scripts: Even though I've been getting better, I just hate it when a script either simply does not work, or under performs.
Rude players: Take a look at the thread for Metapod's AshGray. It really surprised me how some of the players were pretty much going "Screw it, who cares about the hacker? Let's just take his work and build on it!"
Arrogant Hackers: Something I see far too common. Which seriously needs to stop. Your spriting skills are at a professional level? Good for you, but you clearly don't need to flame those that have just begun to sprite and put their badly-drawn sprites in their hacks.
As a player:
Overusing a specific weather condition: Honestly, I don't mind when weather conditions are used, as they give a nice aesthetic feel and helps develop strategy in battle, the problem is when over half of the time in a hack, the weather stays the same. In some hacks I've played, I was pretty much limited to using Fire-type Pokemon only indoors due to constant raining.
Requiring too much HM use: HMs are nice, they serve as decent broken bridges, such as putting bushes on a path to a town that story-wise should not be accessible at the moment. The problem is when the hacker practically requires you to carry HM slaves at all times.
Misusing its/it's and your/you're: For some reason, nothing irks me more than getting the above mixed up. I'm not really picky on grammar, but too many errors can really put me off a hack.
Schizophrenic difficulty: I do like difficult hacks, but I still play easy and average hacks from time to time. What I hate is when the hacker can't seem to decide whether to make his game easy or hard.
Going crazy on 4th/5th Gen mons without proper mechanics: Seriously, it's not that I'm a genwunner or anything like it, but some people just badly implement these later gen mons in their games. In the end, we end up getting useless mons such as Vespiquen without its signiture moves, or an Abomasnow without Snow Warning, or even a Darmanitan with only special moves. Really, can you imagine if someone attempted to put a Shedinja in Gen I or II without its ability?