The data lines won't all change at exactly the same time, so yes, that's your problem.
It might be better to look at half of the data bus at a time. Keep one channel on the clock, one on a signal that will indicate the start of your loop (when I'm bringing up a 6502, I put the start of the loop at an address ending in 1ff, and don't access anything else at an address with bit 8 high. Then I can use the falling edge of A8 as a loop trigger). Capture D0-D3, then D4-D7 in another pass. That leaves a couple of channels for part of the address, or R/W.
It's possible to do this with a 2 channel scope with external trigger and a bit of patience.