That's just MP3, Vorbis and Opus don't have that problem.
E.g. create a full-scale sine wave, split it into two files, then convert them to "gapless" Opus. Now open the files in Audacity and you'll see that there's a small amount of ringing at the boundary, so it is not truly gapless.
If you try the same with AAC using Apple's gapless metadata (i.e. iTunSMPB) you'll find that the boundary is perfectly continuous.