Triple Trouble takes place in the timeline where the non-locked-on Sonic the Hedgehog 3 happened.
Sonic 3, without Sonic & Knuckles locked on, ends with the Death Egg seemingly exploding as it falls, bringing Sonic and Tails Angel Island adventure to an early end, with Triple Trouble being their following adventure.This explains why Knuckles seems to be still working against the duo in the 8-bit title, as he still hasn’t realised he’s been tricked.