For me, the most troublesome kit in recent memory was ICM's 1/72 MiG-31 Foxhound, I've seen some folks get it done to a good standard, though I never got it finished. Fit troubles nose to tail, hard to tell where the flash stops and the parts begin, questionable parts breakdown....
Further back, the kit that takes the cake for total destruction of morale and willingness to see it through to completion in my book is AMT's old 1/48 Bell 222. For those who have made the mistake of purchasing this kit, I feel your pain.
For those who have not tried it, whether you happen upon it as its CHiP version, Airwolf version or its reissued by Hobbycraft Canada version; DON'T touch it! It's pure concentrated evil in a cardboard box.