I'm not fully through the page but I've found at least 8 separate occurrences of the operation "LDY #$00" added in various spots. At first I thought this must have been a case where the original code falsely assumed that Y, or certain status flags, would always have a specific value at that point, and this was a fix for that. But that doesn't seem to be the case.
Attached is a specific example. The code itself has to do w/ the speed of Jason's swimming animation (faster if the D-Pad is pressed). I made a trace log for the original code + the same code with the operation skipped over. This operation doesn't seem to have any direct effect on the following code, since the next relevant values of Y/the status flags are set by other operations afterward.
It's probably not that important but the fact they would go out of their way to add something so specific multiple times makes me wonder what the purpose could possibly be. I was just wondering if it rang a bell for something someone has seen in another game.