I suspect that's what was involved with all the Transfer commands (which are more accurately dubbed "Copy" commands).
As for BEQ/BNE, Gideon's probably right. I just got so used to viewing all CMP's as theoretical subtractions and mentally appending "...to zero" to any subsequent BEQ/BNE. This resulted in much confusion a few weeks back when a BNE command was being skipped despite A, X, and Y all containing non-zero values. (Turns out I'd inserted a JMP patch to a special-handling routine elsewhere, the final portion of which was "CMP #26" with just enough space remaining for the JMP-back. The original routine, not having that special handler, used that BNE as a specific test for the contents of A-reg.)