Spider-Man typically has a solid relationship with most heroes, but Wolverine can sometimes really get on his nerves. This goes even beyond the standard 616 Marvel Universe, as they might arguably have even more problems in the Ultimate Universe. There, Peter Parker was still in high school when his issues with Logan reached their all-time peak. Thanks to Logan being a jerk, Wolverine and Spider-Man wake up one day with their brains in each other's bodies.
The hilarious body swap story comes courtesy of writer Brian Michael Bendis with art by Mark Bagley in Ultimate Spider-Man #66-67. Naturally, it would be pretty wild to go to bed as a high schooler and wake up as a super hairy mutant with metal claws in a dirty hotel room. Peter freaks out, calling his aunt's house and tries to force Logan, now in Peter's body, to go to school. Logan doesn't want to go, telling Peter that school's a waste of time, but Peter needs him to go or else he'll get expelled. Logan finally agrees until Peter can get there so they can figure out how to undo the body swap. Before that happens, however, they both take some time trying to get a handle on each other's powers and abilities.
With Logan's body's enhanced senses, Peter can smell way better than he could in his own, which just makes him realize how much everyone stinks. He also keeps cutting off his fingers, which just heal back, unsure of how to control Logan's claws. Logan on the other hand, keeps sticking to everything and keeps reacting to Peter's spider-sense, making him really jumpy. Eventually they end up making it to each other, but Peter needs Logan to go to a class and get him marked for attendance. While he waits, Peter ends up getting arrested. As a result, Logan has to put on the Peter's Spider-Man mask and tries swinging to the rescue to save Peter. It takes him awhile though, as he's not very good at it. Finally, Logan gets there and knocks out a bunch of cops (much to Peter's horror) and breaks him out.
Once out of the precinct, they try to figure out why and how the body swap happened, but neither of them can come up with a reason. After dealing with the Shocker, which involved a lot of Logan and Peter arguing, the X-Men arrive, after being called by Peter at the precinct as his one phone call. Finally, they figure out what happened: Jean Grey was the one responsible. Having gotten tired with Logan constantly hitting on her, she decided to use her telepathy powers to put Logan's mind in the last place he would want to be, and Logan's subconscious mind chose Spider-Man's body. Obviously, Spider-Man isn't too happy...at all. Jean puts their minds back in their own bodies, but Peter's got some choice to say all the same before he takes off.
It certainly seems like Peter is justified in cussing Logan and the X-Men out, at least in this universe. He's a young high schooler who's trying to do all he can to manage all of his responsibilities at school, to his aunt, his girlfriend, his job at the Daily Bugle, and above all: his powers as Spider-Man. It's a lot for him to deal with, but he's dealing with it as best he can. Then there's the X-Men, who were using their powers pretty irresponsibly like Jean Grey does just to teach Wolverine a lesson, and Peter was paying for it. All in all, the two-part story is super funny and comical, but it's a perfect reason for why Spider-Man doesn't always dig Wolverine or the X-Men for that matter.