It does, indeed, sound like phasing issues,... the way you describe it.
No, it shouldn't happen, but what "should" or "shouldn't" happen in theory, often differs slightly from what "does" happen, in the real world.
Technically, there should be no phase issues between BUSS-L & BUSS-R, GROUP 1/3 & 2/4, on tracks grouped [1-4] and [5-8], ESPECIALLY if you're recording all 4 tracks simultaneously. Any deviation from those basic guidelines, and your results may vary.
What exactly,... or why you're getting this slight phasiness of your sound, is a bit mysterious, but I'd recommend more investigation into the signal chain, technique, & things like that. Hopefully, you're using the internal Busses for routing any similarly paired tracks, and NOT external patch cables, to route your sound around-&-about, to the 4-target tracks. [internal routing = key point].
Certain things like that,... technique & signal chain,... are hard to determine, sight unseen, over a bbs. I'd recommend further troubleshooting to determine what's causing it, or abandoning the technique altogether, if it's not a viable solution.
You're right though,... given that I'm making certain assumptions that all else is "normal" or "standard" configuration,... you "shouldn't" be getting phase issues on a 488mkII, when recording simultaneously to tracks [1-4] and [5-8], or any other combination of 4-tracks [range: 1-8], when RECORDED SIMULTANEOULY. [simultaneously = key point].
I also read the 488mkII recordist's article in Tape Op, and I own & understand the 488mkII,... just as qualifiers.
FYI: Any deviation from "normal" or "standard" patching and routing techniques, and all bets are off, as far as what you could expect to get as the coherency of the resulting recorded sound.