I don't understand what you mean, each gpio input node specifies the pin, so there is no confusion as to which pin it is coming from that node. If you have two pins they will come down different wires so again there is no confusion.
Also note that the gpio pin sets the topic to tell you which pin it is, so if you were to use a Join node to comine them then you can identify them by the topics.
If that doesn't help then explain more about what you are doing.
Just to further iterate on what @Colin wrote. When you get a message from a gpio node it will include a topic like this:
If you connect the output from two gpio nodes to one function node you will have to save the input value as the function node will only ever operate on the message it just received.
So to compare values coming from two different nodes to one function node you will have to use context storage which you can read about here:
This explains the general concepts but there is also a link at the bottom which links to how to use this in a function node.
Work through this.
Once you have grasped this you can than do the following in a function node:
if topic is pin 33 -> save to context as 33 and get the stored value for 32
if topic is pin 32 -> save to context as 32 and get the stored value for 33
compare the incoming value to the other value you retrieved from context with an if else statement based on your needs
return a output message based on this if condition
To write this code you will need the following JavaScript and nodered skills:
working with context in functions:
if conditions:
Feel free to ask if you get stuck applying those concepts.