At least for me there could be two buckets. One where a highly ranked player didn't pan out versus a team taking somebody unexpected and then it didn't work out. OP seems to want the latter.
1995 was the first draft I watched, but I probably wasn't following closely until I got internet access in 1997. If only for the excuse to walk down memory lane:
1995: Teemu Riihijarvi (12th overall) - San Jose was entering the final year of the weird management setup where Dean Lombardi and Chuck Grillo were essentially co-GMs. Grillo had a fascination with European players. He wasn't necessarily wrong as they hit on some later picks, but in this case the Sharks went for a toolsy 6'5 forward. Although according to an article from the time, the Islanders apparently had a deal in place for #15 and were targeting Riihijarvi as well. Scottie Bowman also congratulated the Sharks on the pick.
1998: Mike Rupp (9th overall) - Maybe similar to Riihijarvi, Rupp was a toolsy power forward who didn't have the production. There had been rumblings that Rupp would go higher on draft day since it was a middling draft class and he had higher theoretical upside. Nik Antropov (ranked #53 by THN) went #10 for similar reasons.
According to the draft broadcast, the Islanders table was debating between Rupp and Robyn Regehr at #9. Presumably since they were loaded with young D, they went with Rupp who'd they chose not to sign by 2000. Rupp would get re-drafted in the third round and he'd have a decent enough career as a bottom six role player.
2001: Adrian Foster (28th overall) - Maybe not as high of expectations for a late 1st, but apparently the Devils didn't love the crop and decided to take a home run swing. Foster had only played in 12 WHL in the previous two seasons combined due to injuries. When he was younger, he held his own with Dany Heatley and Krys Kolanos (who was looking good at this point in 2001). According to Gare Joyce's book "Future Greats and Heartbreaks", New Jersey knew they had a 2003 2nd round pick as compensation in their back pocket if they didn't sign Foster. But they'd end up signing him and Foster didn't pan out as he battled through a myriad of injuries as a pro.
Although with hindsight there wasn't that much to lose sleep over. I just remember the confusion on the broadcast as there was a delay. I forget if the pick was so unexpected that Central Registry had to double check that Foster's paperwork was in order.