As OkiePC and BitBucket pointed out it was probably done to "fix/bypass" a problem or alter a standard template. But there are problems with handling such this way 1) it makes it hard to deterrmine if this was actually done to fix or bypass a problem or alter a standard template, 2) it makes it hard to determine what the normal state of B3:4/9 is suppose to be, 3) it's hard to find these "logic bypasses" in the program and 4) it's hard to figure out if the program has any "logic bypasses" in it at all. There is a better way to handle such issues.
The first rung of all my programs is a bit that is always off called DisabledLogic. The rung comment is - "Disabled Logic bit is used in the program where logic is temporary disabled. Disabled Logic bit allows the programmer to quickly find disabled logic. Disabled Logic bit is NOT used for default programming". Now if someone opens one of my programs, even myself, you can quickly do a search for DisabledLogic and determine if any logic in the program has be "temporary" disabled for some reason. Not only that but knowing the DisabledLogic bit is always off, someone should be able to figure out what the issue is/was by seeing how the DisabledLogic bit is used in the rung. Plus I usually add a comment to the rung as to why it was done.
When it comes to altering a standard template I use the PLC's AlwaysOn and AlwaysOff bits. It makes it easy to see what is altered in the standard template.